Inhibitors of autoinducer transporters

ABSTRACT

The present invention relates to the discovery of the lsr operon, the genes therein, and the polypeptides encoded by these genes. The present invention also includes strains with altered expression levels of the polypeptides encoded by the genes and the lsr operon relative to wild type cells. In some embodiments, the strains express a transporter that transports an autoinducer into the cell at a level higher than that of wild type cells. The present invention also includes methods for identifying compounds that modulate the transport of the autoinducer into cells.

RELATED APPLICATION INFORMATION

This application claims priority to U.S. Provisional Application No.60/336324, filed on Oct. 26, 2001 and entitled Inhibitors of AutoinducerTransporters, the disclosure of which is hereby incorporated byreference in its entirety.

STATEMENT OF GOVERNMENT INTEREST

The National Science Foundation Grants MCB-0083160, MCB-0094447, and.MCB-9506033 and The Office of Naval Research Grant Number N00014-99-0767supported this work. Accordingly, the U.S. Government has certain rightsin this invention.

BACKGROUND OF THE INVENTION

Several publications are referenced in this application to more fullydescribe the state of the art to which this invention pertains. Theentire disclosure of each such publication is incorporated by referenceherein.

Bacteria regulate gene expression in response to changes in cellpopulation density by a process called quorum sensing. Specifically,quorum sensing bacteria release and detect chemical signals calledautoinducers. Bacteria respond to the accumulation of a minimalthreshold stimulatory concentration of autoinducer. Detection ofautoinducers enables bacteria to distinguish between low and high cellpopulation density, and to control target gene expression in response tofluctuations in cell number. Quorum sensing bacteria regulate processesthat require the cooperation of a number of bacterial cells in order tobe effective, and the individuals in the group profit from the activityof the entire assembly (Bassler, 1999; Fuqua et al., 1996; Kleerebezemet al., 1997; Lazazzera and Grossman, 1998; Miller and Bassler, 2001;Schauder and Bassler, 2001; de Kievit and Iglewski, 2000). Theseprocesses include bioluminescence, virulence, antibiotic production,sporulation and biofilm formation. Quorum sensing therefore allows apopulation of bacteria to coordinate behavior, and thus take on thecharacteristics of multi-cellular organisms.

In general, quorum sensing is controlled by acyl-homoserine lactoneautoinducers in Gram-negative bacteria and by modified oligopeptideautoinducers in Gram-positive bacteria (Miller and Bassler, 2001;Schauder et al., 2001; Lazazzera and Grossman, 1998; de Kievit andIglewski, 2000). Gram-negative quorum sensing circuits typicallyresemble the canonical circuit of Vibrio fischeri. Specifically, theacyl-HSL autoinducer synthase is similar to the V. fischeri Luxl enzyme,and a transcriptional activator similar to the V. fischeri LuxR proteinis responsible for autoinducer recognition and target gene activation(Engebrecht et al., 1983; Engebrecht and Silverman, 1984; 1987; Millerand Bassler, 2001; de Kievit and Iglewski, 2000). In Gram-positivebacteria, the oligopeptide autoinducers are synthesized as precursorpeptides that are processed, modified and subsequently secreted by ATPBinding Cassette (ABC) type exporters. Gram-positive bacteria detect andrespond to oligopeptide autoinducers via two-component phosphorylationcascades (Kleerebezem et al., 1997; Lazazzera and Grossman, 1998; Millerand Bassler, 2001). Both acyl-HSL and oligopeptide autoinducers arehighly specific to the species that produce them, as autoinducersproduced by one species usually do not influence expression of genes inother species. It is remarkable that such signaling specificity existsin both types of quorum sensing circuits, given the similarity in themembers of each class of signal.

Unlike all other quorum sensing bacteria, Vibrio harveyi, abioluminescent Gram-negative bacterium, uses a novel regulatory circuitto control quorum sensing. Specifically, V. harveyi controls densitydependent expression of the luciferase genes using a hybrid quorumsensing circuit, with components common to both Gram-negative andGram-positive quorum sensing systems (Bassler, 1999). Like otherGram-negative quorum sensing bacteria, V. harveyi uses anacyl-homoserine lactone autoinducer (called AI-1) as a signal (Bassleret al., 1993; Cao and Meighen, 1989). However, similar to Gram-positivequorum sensing bacteria, V. harveyi employs a two-component signalingcircuit for autoinducer detection and signal transduction (Bassler etal., 1993; Bassler et al., 1994a; b; Freeman and Bassler, 1999a; b;Freeman et al., 2000; Lilley and Bassler, 2000). In addition, a second,novel autoinducer, termed AI-2, also regulates quorum sensing in V.harveyi (Bassler et al., 1994a; Surette and Bassler, 1998; Surette etal., 1999). It is hypothesized that V. harveyi uses AI-1 forintra-species cell-cell communication and AI-2 for inter-speciescell-cell signaling (Bassler et al., 1997; Bassler, 1999; Surette etal., 1999). These distinct signals presumably allow V. harveyi, whichinhabits multi-species consortia, to vary its gene expression not onlyin response to changes in total cell number, but also in response tofluctuations in the species composition of the community.

Thus, V. harveyi has two independent density sensing systems (calledSignaling Systems 1 and 2), and each is composed of a sensor-autoinducerpair. V. harveyi Signaling System 1 is composed of Sensor 1 andautoinducer 1 (AI-1), and this autoinducer isN-(3-hydroxybutanoyl)-L-homoserine lactone (see Bassler et al., Mol.Microbiol. 9: 773-786, 1993). V. harveyi Signaling System 2 is composedof Sensor 2 and autoinducer 2 (AI-2) (Bassler et al., Mol. Microbiol.13: 273-286, 1994). Signaling System I is a highly specific systemproposed to be used for intra-species communication and Signaling System2 appears to be less species-selective, and is hypothesized to be forinter-species communication (Bassler et al., J. Bacteriol. 179:4043-4045, 1997). Reporter strains of V. harveyi have been constructedthat can produce light exclusively in response to AI-1 or to AI-2(Bassler et al., 1993, supra; Bassler et al., 1994, supra).

Quorum sensing in V. harveyi, mediated by Signaling Systems 1 and 2,triggers the organisms to bioluminesce at a certain cell density. Thesesame signaling systems, particularly Signaling System 2, are believed totrigger other physiological changes in V. harveyi and other bacteriapossessing the same signaling system.

Consistent with a role for AI-2 as a universal signal used for bacterialinter-species communication, over 30 species of Gram-negative andGram-positive bacteria have now been shown to produce AI-2 (Bassler etal., 1997; Miller and Bassler, 2001; Surette and Bassler, 1998, thedisclosures of which are incorporated herein by reference in theirentireties). In every case, an AI-2 synthase that is highly homologousto the V. harveyi AI-2 synthase called LuxS is required for AI-2production (Surette et al., 1999). Recently, the biosynthetic pathwayfor AI-2 synthesis was described (Schauder and Bassler, 2001; Schauderet al., 2001). AI-2 is produced from S-ribosylhomocysteine (SRH), aproduct in the S-adenosylmethionine (SAM) utilization pathway.Specifically, LuxS cleaves SRH to form homocysteine and AI-2. Althoughnot confirmed, AI-2 appears to be a furanone with structural similarityto ribose (Schauder et al., 2001). The current evidence suggests that,in contrast to the variable structures of acyl-homoserine lactone andpeptide autoinducers, the structures of AI-2 from different species ofbacteria are identical. If AI-2 is used for inter-species signalling innatural habitats, a common signal structure could be required for it tobe recognized by multiple members of a mixed-species community (Schauderet al., 2001; Schauder and Bassler, 2001).

Although the role of AI-2 is understood in the regulation ofbioluminescence in V. harveyi, what function AI-2 plays, if any, inother luxS-containing bacteria is not clear. There are reports showingthat AI-2 is involved in regulating type III secretion in E. coli0157:H7 (Sperandio et al., 1999), protease production in Streptococcuspyogenes (Lyon et al., 2001), hemolysin production in V. vulnificus (Kimet al., 2000), and regulation of the virulence factor VirB in Shigellaflexneri (Day and Maurelli, 2001). Genetic experiments established howAI-2 regulates gene expression in Salmonella typhimurium, and show thatAI-2 controls the expression of a previously uncharacterized operonencoding an ABC transporter apparatus that appears to function in theuptake of AI-2.

Definitions:

Various terms relating to the biological compounds of the presentinvention are used throughout the specifications and claims. The terms“substantially the same,” “percent similarity” and “percent identity”are defined in detail below.

The novel signaling factor of the present invention is alternativelyreferred to herein as “signaling factor”, “signaling compound”,“autoinducer”, and more specifically, “autoinducer-2” or AI-2”. Theterms “autoinducer-2” and “AI-2” refer specifically to the signalingfactor as produced by Vibrio harveyi. The terms “signaling factor” or“signaling compound”, “autoinducer” or “AI-2-like compound” refergenerally to the signaling factors of the present invention, of whichAI-2 is an example.

The term “isolated nucleic acid”, when applied to DNA, refers to a DNAthat is separated from sequences with which it is immediately contiguous(in the 5′ and 3′ directions) in the naturally occurring genome of theorganism from which it was derived. For example, the “isolated nucleicacid” may comprise a DNA inserted into a vector, such as a plasmid orvirus vector, or integrated into the genomic DNA of a procaryote oreucaryote. An “isolated nucleic acid” may also comprise a cDNA.

The term “isolated nucleic acid”, when applied to RNA, refers to an RNAencoded by an isolated DNA as defined above. Alternatively, the term mayrefer to an RNA that has been sufficiently separated from RNAs withwhich it would be associated in its natural state (i.e., in cells ortissues), such that it exists in a “substantially pure” form (the term“substantially pure” is defined below).

The term “isolated protein” or “isolated and purified protein” refersprimarily to a protein produced by expression of an isolated nucleicacid of the invention. Alternatively, this term may refer to a proteinthat has been sufficiently separated from other proteins with which itwould naturally be associated, so as to exist in “substantially pure”form.

The term “substantially pure” refers to a preparation comprising atleast 50-60% by weight the factor of interest (e.g., pathogenesissignaling factor, nucleic acid, oligonucleotide, protein, etc.). Morepreferably, the preparation comprises at least 75% by weight, and mostpreferably 90-99% by weight, the factor of interest. Purity is measuredby methods appropriate for the factor of interest (e.g. chromatographicmethods, agarose or polyacrylamide gel electrophoresis, HPLC analysis,and the like).

With respect to antibodies of the invention, the term “immunologicallyspecific” refers to antibodies that bind to one or more epitopes of aprotein of interest, but that do not substantially recognize and bindother compounds in a sample containing a mixed population of antigenicbiological constituents.

With respect to oligonucleotides, the term “specifically hybridizing”refers to the association between two single-stranded nucleotides ofsufficiently complementary sequence to permit such hybridization underpre-determined conditions generally used in the art (sometimes termed“substantially complementary”). In particular, the term refers tohybridization of an oligonucleotide with a substantially complementarysequence contained within a single-stranded DNA or RNA of the invention,to the substantial exclusion of hybridization of the oligonucleotidewith single-stranded nucleic acids of noncomplementary sequence.

The term “promoter region” refers to the transcriptional regulatoryregions of a gene, which may be found at the 5′ or 3′ side of the codingregion, or within the coding region, or within introns. The term“selectable marker gene” refers to a gene encoding a product that whenexpressed, confers a selectable phenotype such as antibiotic resistanceon a transformed cell.

The term “reporter gene” refers to a gene that encodes a product that iseasily detectable by standard methods, either directly or indirectly.

The term “operably linked” means that the regulatory sequences necessaryfor expression of the coding sequence are placed in the DNA in theappropriate positions relative to the coding sequence so as to enableexpression of the coding sequence. This same definition is sometimesapplied to the arrangement of transcription units and other regulatoryelements (e.g., enhancers or translation regulatory sequences) in anexpression vector.

The term “wild type cell” or “wild type strain” is used herein todescribe cells or strains that serve as a reference point for cells orstrains in which the expression level of a particular protein has beenaltered (i.e increased or decreased). Generally, the “wild type cell” or“wild type strain” and the cell or strain to which it is being comparedwill have the same genotype except for one or more difference thatchange the expression level of the as used herein “wild type cells” or“wild type strains” may contain certain mutations that are shared withthe cells or strains to which they are being compared but they do notshare the genotype that confers altered expression levels of the proteinof interest. For example, if a strain or cell expresses a higher levelof a transporter than a wild type strain or cell, it may be geneticallyidentical to the wild type strain or cell except for one or moremutations that are responsible for the increased expression level of thetransporter.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Signaling substance from E. coli AB1157 and S. typhimurium LT2cell-free culture fluids that induces luminescence in V. harveyi. Theresponses of V. harveyi reporter strains BB170 (Sensor 1⁻, Sensor 2⁺)(FIG. 1A), and BB886 (Sensor 1⁺, Sensor 2⁻) (FIG. 1B) to signalingsubstances present in cell-free culture fluids from E. coli, S.typhimurium and V. harveyi strains are shown. A bright culture of eachreporter strain was diluted 1:5000 into fresh medium, and the lightproduction per cell was then measured during the growth of the dilutedculture. Cell-free culture fluids or sterile growth medium were added ata final concentration of 10% (v/v) at the start of the experiment. Thedata for the 5 hour time point are shown and are presented as thepercent of the activity obtained when V. harveyi cell-free spent culturefluids are added. Abbreviations used for the different strains are: V.h;Vibrio harveyi, S.t; Salmonella typhimurium, and E.c; Escherichia coli.

FIG. 2. Active secretion of the signaling compound by viable E. coli andS. typhimurium. The response of the V. harveyi reporter strain BB170(Sensor 1⁻, Sensor 2⁺) to a signaling substance produced and secreted byE. coli AB1157 and S. typhimurium LT2 but not E. coli DH5 is shown. V.harveyi reporter strain BB170 was diluted 1:5000 in AB medium and lightoutput per cell was monitored during growth. At the start of theexperiment, either 1×10⁶ E. coli AB1157, S. typhimurium LT2 or E. coliDH5 washed and resuspended viable cells (left-hand, white bars) orUV-killed cells (right-hand, black bars) was added. The data arepresented as the fold-activation above the endogenous level ofluminescence expressed by V. harveyi BB170 at the 5 hour time point.Abbreviations used for the different strains are: S.t; Salmonellatyphimurium, and E.c; Escherichia coli.

FIG. 3. Effect of glucose depletion on the production and degradation ofthe signaling activity by S. typhimurium LT2. S. typhimurium LT2 wasgrown in LB medium containing either 0.1% glucose (FIG. 3A) or 0.5%glucose (FIG. 3B). At the specified times cell-free culture fluids wereprepared and assayed for signaling activity in the luminescencestimulation assay (Bars), and the concentration of glucose remaining(circles). The cell number was determined at each time by diluting andplating the S. typhimurium LT2 on LB medium and counting colonies thenext day (squares). The signaling activity is presented as the percentof the activity obtained when V. harveyi cell-free spent culture fluidsare added. These data correspond to the 5 h time point in theluminescence stimulation assay. The glucose concentration is shown as %glucose remaining. Cell number is cells/ml×10⁻⁹. The symbol\\indicatesthat the time axis is not drawn to scale after 8 h.

FIG. 4. Response curve of V. harveyi to AI-2 produced by V. harveyi andS. typhimurium. The V. harveyi reporter strain BB170 (Sensor 1⁻, Sensor2⁺) was tested for its response to the addition of exogenous AI-2 madeby V. harveyi strain BB152 (AI-1⁻, AI-2⁺) and to that made by S.typhimurium LT2. A bright culture of the reporter strain was diluted1:5000 and either 10% (v/v) growth medium (closed circles), cell-freeculture fluid from V. harveyi BB152 grown overnight in AB (opencircles), or cell-free culture fluid from S. typhimurium LT2 grown for 6h on LB+0.5% glucose (closed squares) was added at the start of theexperiment. RLU denotes relative light units and is defined as (countsmin⁻¹×10³)/(colony-forming units ml⁻¹).

FIG. 5. Conditions affecting autoinducer production in S. typhimurium.S. typhimurium LT2 was subjected to a variety of treatments after whichcell-free culture fluids or osmotic shock fluids were prepared. Thesepreparations were added to a diluted culture of the V. harveyi AI-2reporter strain BB170 at 10% (v/v) and light output was measuredthereafter. Fold activation is the level of light produced by thereporter following addition of the specified S. typhimurium preparationdivided by the light output of the reporter when growth medium alone wasadded. The bars in FIG. 5A represent cell-free fluids prepared from S.typhimurium after the following treatments: LB 6 h; 6 h growth in LB at30° C., LB+Glc 6 h; 6 h growth in LB+0.5% glucose at 30° C., LB+Glc 24h; 24 h growth in LB+0.5% glucose at 30° C. In all the experimentspresented in FIG. 5B, the S. typhimurium were pregrown at 30° C. for 6 hin LB containing 0.5% glucose, then pelleted and resuspended for 2 hunder the following conditions: LB; in LB at 30° C., LB+Glc; in LB+0.5%glucose at 30° C., LB pH 5; in LB at pH 5.0 at 30° C., 0.4 M NaCl; in0.4 M NaCl at 30° C., 0.1 M NaCl; in 0.1 M NaCl at 30° C., and HeatShock 43°; in LB+0.5% glucose at 43° C. After these two hour treatments,cell-free fluids were prepared from each sample and assayed.

FIG. 6. S. typhimurium signaling activity in limiting and non-limitingconcentrations of glucose. S. typhimurium LT2 was grown in LB in thepresence of limiting (0.1%) and non-limiting (1.0%) concentrations ofglucose. The activity present in the cell-free culture fluids (blackbars) was assayed at the times indicated and normalized to that producedby 1×10⁹ cells. The increase in signaling activity measured in the 0.4 MNaCl osmotic shock fluids prepared from the same cells is shown as thewhite bars on top of the black bars. These data are also normalized for1×10⁹ cells. The signaling activity for limiting glucose is shown inFIGS. 6A, 6C, and 6E, and that for non-limiting glucose is shown inFIGS. 6B, 6D, and 6F. FIGS. 6A and 6B also show the percent glucoseremaining (triangles), FIGS. 6C and 6D show the cell number (squares),and Panels E and F show the pH (circles) at each time point.

FIG. 7. Effects of glucose and pH on signal production by S.typhimurium. The quorum sensing signal released by S. typhimurium LT2was measured when the cells were grown in LB medium containing 0.5%glucose at pH 7.2 (FIG. 7A, bars), and when the cells were grown in LBat pH 5.0 without an added carbon source (FIG. 7B, bars). The level ofsignal present in cell free culture fluids (black bars) and in 0.4 MNaCl osmotic shock fluids was measured (white bars on top of black bars)at the time points indicated. In each panel, the circles represent thepH of the medium, and the squares show the cell number at the differenttime points.

FIG. 8. High osmolarity induces signal release and low osmolarityinduces signal degradation in S. typhimurium LT2. The quorum sensingsignal released by S. typhimurium LT2 resuspended in 0.4 M NaCl and in0.1 M NaCl was measured in the presence and absence of proteinsynthesis. S. typhimurium LT2 was pre-grown in LB containing 0.5%glucose for 6 h. The cells were harvested and resuspended in 0.4 M NaCl(FIG. 8A) or 0.1 M NaCl (FIG. 8B) in the presence or absence of 30 g/mlCm for the time periods indicated. In each panel, the open symbolsrepresent the activity measured in the absence of Cm and the closedsymbols represent the activity measured in the presence of Cm.

FIG. 9. The luxS and ygaG genes from V. harveyi and E. coli MG1655. FIG.9A shows a restriction map of the V. harveyi luxS_(V.h.) chromosomalregion that was defined by Tn5 insertion. The sites of Tn5 insertionsthat disrupted the AI-2 production function and one control Tn5insertion outside of the luxS_(V.h.) locus are shown (triangles). FIG.9B depicts the ygaG region in the E. coli MG1655 chromosome. This ORF isflanked by the emrB and gshA genes. The direction of transcription ofeach gene is indicated by the horizontal arrows. The correspondingposition of the MudJ insertion that eliminated AI-2 production in S.typhimurium LT2 is shown by a vertical arrow. H, R, P, and B denoteHindIII, EcoRI, PstI and BamHI restriction sites respectively.

FIG. 10. Autoinducer production phenotypes of V. harveyi and S.typhimurium strains. Cell-free culture fluids from V. harveyi and S.typhimurium strains were prepared and tested for AI-2 activity in the V.harveyi BB170 bioassay. FIG. 10A: AI-2 production phenotypes of the wildtype V. harveyi strain MM28 that contains a Tn5 insertion outside ofluxS_(V.h.) (denoted WT) and the luxS_(V.h.)::Tn5 mutant strain MM30(denoted luxS⁻). FIG. 10B: AI-2 production phenotypes of wild type S.typhimurium LT2 (denoted WT) and the ygaG::MudJ insertion mutant strainCS132 (denoted ygaG⁻). Activity is reported as fold-induction ofluminescence expression of the V. harveyi BB170 reporter strain overthat when sterile medium was added.

FIG. 11. Complementation of AI-2 production in S. typhimurium CS132 andE. coli DH5. Cell-free culture fluids from E. coli and S. typhimuriumstrains were tested for AI-2 activity in the bioassay. The activitypresent in these fluids was compared to that produced by wild type V.harveyi BB120. In the figure, the level of BB120 activity was normalizedto 100%. : AI-2 activity in cell-free fluids from wild type V. harveyiBB120, E. coli O157:H7, and S. typhimurium LT2.

FIG. 12 Complementation of S. typhimurium CS132 (ygaG::MudJ) (panel A)and of E. coli DH5 (panel B). The in trans AI-2 production genes are thefollowing: vector control (denoted: none), E. coli O157:H7 ygaG; and V.harveyi BB120 luxS_(V.h.) E. coli and V. harveyi are abbreviated E.c.and V.h. respectively.

FIG. 13. Alignment of LuxS and YgaG protein sequences. The translatedprotein sequences for the AI-2 production family of proteins are shown.We determined the sequences for the luxS_(V.h.) gene from V. harveyiBB120 (SEQ ID NO:10), and the ygaG (renamed herein as luxS_(E.c.) fromE. coli MG1655 (SEQ ID NO: 11), E. coli 0157:H7 (SEQ ID NO: 11), and E.coli DH5 (SEQ ID NO: 18). The S. typhimurium LT2 ygaG (renamed hereinluxS_(S.t.) partial sequence (SEQ ID NO: 12) came from the S.typhimurium database. Amino acid residues that are not identical to theLuxS_(V.h.) protein are underlined and not in bold font. The site of theframe shift mutation in the E. coli DH5 DNA sequence is denoted by an“*”. The 20 altered amino acid residues that are translated followingthe frame shift are enclosed by the box.

FIG. 14. A diagram of the hybrid quorum sensing circuit of Vibrioharveyi is provided. The AI-1 and AI-2 circuits are independentlystimulated but integrate their signals for light expression. Eachpathway, however, is also independently competent to general light. Thisallows for reciprocal mutations in the LuxN or LuxQ sensors to be usedto construct a reporter specific for AI-2 or AI-1, respectively.

FIG. 15. Response phenotypes of V. harveyi wild-type and lux regulatorymutants. At the first time point, cell-free culture fluids (10%), ornothing (N.A) was added typed-type, cell-free culture fluid (AI-1+AI2);LuxS⁻ cell-free culture fluid (AI-1); LuxM⁻ cell-free culture fluid(AI-2). Relative light units are defined as cpm×10³/CFU/ml.

FIG. 16. A diagram of the biosynthetic pathway of autoinducer-2 (AI-2),including the structure of AI-2, is shown.

FIG. 17 shows the Isr and rbs Operons of S. typhimurium. Panel A: Thelsr operon of S. typhimurium contains genes homologous to the transportcomponent of the rbs operon (Panel B). In Panel A, triangles denote thesites of the MudJ insertions, with strain names above. A gene calledlsrR is transcribed divergently from the lsr operon and encodes aprotein (LsrR) required for AI-2 regulation of the lsr operon (seetext). Panel B: The rbsDACBKR operon of E. coli and S. typhimuriumencodes proteins required for the high affinity transport andphosphorylation of ribose. rbsD encodes a protein of unknown function.The ABC transport apparatus is encoded by rbsACB. rbsK encodes thecytoplasmic ribokinase, which phosphorylates ribose. rbsR encodes arepressor protein that regulates transcription of the rbs operon. Inboth panels, black boxes represent promoters, and thin arrows indicatethe direction of transcription. Panel C: A schematic of the ribosetransport system is shown. Similar shading patterns indicate homologousgenes in panels A and B, and protein functions in panel C.

FIG. 18 shows luxS regulates the transcription of the Isr operon. Theβ-galactosidase activity is shown for five MudJ-lacZ reporter fusions ingenes in the lsr operon. The white and black bars show the activity forthe Isr::MudJ fusions in luxS::T-POP (denoted luxS null) and wild typeluxS backgrounds, respectively. The gray and striped bars show theactivity when the plasmids pUC18 (parental vector) and pAB15 (pUC18expressing wild type luxS) were introduced into the luxS::T-POP strains,respectively.

FIG. 19 shows how AI-2 regulates Isr operon expression. Theβ-galactosidase activity of strains carrying MudJ fusions in five Isrgenes was assayed in luxS::T-POP (denoted luxS null) and wild type luxSbackgrounds. Cultures were grown in LB containing either a controlreaction mixture (denoted−AI-2) or in vitro synthesized AI-2(denoted+AI-2). In vitro AI-2 was prepared by incubatingS-adenosylhomocysteine and the purified Pfs and LuxS proteins asdescribed by Schauder et al. (in press). The control mixture (−AI-2) wasprepared by an identical procedure except that the reaction was carriedout the absence of LuxS protein. (D,L)-homocysteine was added to thiscontrol preparation following the reaction to compensate for thehomocysteine produced in the reaction containing LuxS. AI-2 was used atan estimated concentration of 70 μM in this experiment.

FIG. 20 shows that AI-2 control of Isr operon expression requires theLsrR protein. β-galactosidase activity was measured from the lsrC::MudJreporter in wild type lsrR and ΔlsrR S. typhimurium strains.Additionally, the β-galactosidase activity was measured in these samestrains following the introduction of the vector pMET1035 that carriesthe wild type lsrR gene (denoted plsrR). The white bars show theactivities in a luxS null S. typhimurium strain background and the blackbars show the activities in a wild type luxS S. typhimurium strainbackground.

FIG. 21 shows the activity of LsrR suppressor mutants. Eight spontaneousmutations in lsrR were identified that conferred a Lac⁺ phenotype to anS. typhimurium lsrC::MudJ, luxS null strain. The LsrR protein sequenceand the amino acid alterations causing a suppressor phenotype are shown.The spontaneous deletion that resulted in a suppressor phenotype isshown by a single underline (denoted Δ5′). The predictedhelix-turn-helix DNA binding motif is shown by the double underline.

FIG. 22 shows the corresponding β-galactosidase activity for thelsrC::MudJ reporter in each of the eight suppressor strains and theactivity for one of the lsrR::T-POP suppressors we obtained. In everycase, the chromosomal copy of the luxS gene has been inactivated byinsertion. As a reference, the β-galactosidase activity from thelsrC::MudJ reporter is also shown for S. typhimurium strains containingthe wild type lsrR gene (controls) and an in-frame deletion of lsrR(denoted ΔlsrR).

FIG. 23 shows that removal of AI-2 from S. typhimurium culture fluidsrequires the Lsr ABC transporter. The figure shows the quantity of AI-2remaining in cell-free culture fluids of S. typhimurium strainscontaining various mutations in lsr genes. AI-2 activity in the culturefluids was measured through use of the V. harveyi BB170 AI-2 bioassay.All strains tested contained a null mutation in luxS, so the only AI-2present was that that was added exogenously. Various S. typhimuriumstrains were grown for 4 h. In vitro prepared AI-2 was included in thecultures during the final hour of growth. The control bar represents theAI-2 activity for the culture fluid of the S. typhimurum luxS nullparent strain SS007 (luxS::T-POP) when no AI-2 was added. The input barrepresents the amount of AI-2 activity added to each culture. The restof the bars show the AI-2 activity remaining in the culture fluids ofthe wild type lsr strain and the various lsr mutants following the 1 hincubation period.

FIG. 24 Time courses of elimination of AI-2 from the culture fluids areshown for the wild type lsrR strain SS007 (luxS::T-POP, Triangles) andthe ΔlsrR strain MET342 (ΔlsrR, luxS::T-POP, Circles). These cultureswere grown for a total of 4 h. During the final hour of growth, AI-2 wasincluded in the cultures for the times specified on the X-axis.

FIG. 25 shows a model for regulation and function of the Lsr ABCtransporter in S. typhimurium. In the absence of AI-2, the LsrR DNAbinding protein represses transcription of the lsr operon. LuxSsynthesizes AI-2 (black pentagons), and AI-2 is released from the cellby an unknown mechanism. External AI-2 signals to the LsrR protein. Thisstep inactivates the LsrR repressor function, which promotestranscription of the lsr operon. The mechanism of AI-2 signalling toLsrR is not known, but we propose that a sensor exists that couples AI-2detection to LsrR activity. The white box containing the question markrepresents the putative sensor. Transcription of the lsr operon resultsin the production of the Lsr ABC transporter complex that functions toimport AI-2 into S. typhimurium. In the figure, the LsrACBD componentsare shown as the complex in the bacterial membrane. We hypothesize thatAI-2 interacts with the periplasmic LsrB protein (represented by thestippled oval), and that LsrB-AI-2 binding facilitates interaction withthe channel and ATPase components of the Lsr complex for transport. Notethat the ABC transporter is predicted to reside in the inner-membranewith LsrB in the periplasm (gray and striped boxes). In the figure wehave not drawn the outer-membrane of the bacterial cell.

SUMMARY OF THE INVENTION

Some aspects of the invention are described in the following numberedparagraphs:

1. An isolated bacterial strain having an increased expression level ofa transporter that transports an autoinducer into the strain relative toa wildtype strain, wherein the autoinducer is not an acyl-homoserinelactone and can interact with the Vibrio harveyi LuxQ protein, therebyinducing expression of a Vibrio harveyi operon comprising the luxCDABEgenes.

2. The strain of Paragraph 1, wherein the strain has been geneticallyengineered to increase expression of the transporter.

3. The strain of Paragraph 1, wherein the transporter comprises at leastone polypeptide comprising a sequence selected from the group consistingof SEQ ID NOs.: 37-40 and a sequence having at least 25% amino acididentity as determined through use of FASTA version 3.0t78 with thedefault parameters to one of SEQ ID NOs.: 37-40.

4. The strain of Paragraph 1, wherein the transporter comprises acomplex comprising each of the sequences of SEQ ID NOs. 37-40 orsequences having at least 25% identity as determined through use ofFASTA version 3.0t78 with the default parameters to each of thesequences of SEQ ID NOs.: 37-40.

5. The strain of Paragraph 2, wherein the strain comprises at least onevector from which one or more polypeptides included in the transporterare expressed.

6. The strain of Paragraph 1, wherein the strain comprises a mutationthat increases expression of the transporter.

7. The strain of Paragraph 6, wherein the mutation is in a gene encodinga repressor that reduces expression of the transporter.

8. The strain of Paragraph 7, wherein the mutation is in a genecomprising the sequence of SEQ ID NO: 28.

9. The strain of Paragraph 8, wherein the mutation is in a genecomprising a sequence having at least 30% identity to SEQ ID NO: 28 asdetermined through use of BLASTN version 2.0 with the defaultparameters.

10. The strain of Paragraph 7, wherein the mutation is in a geneencoding a polypeptide comprising the sequence of SEQ ID NO: 36.

11. The strain of Paragraph 7, wherein the mutation is in a nucleic acidcomprising a sequence that hybridizes to a probe comprising at least 30consecutive nucleotides of SEQ ID NO: 28 in 6×SSC at about 45° C.followed by one or more washes in 0.1×SSC/0.2% SDS at about 68° C.

12. The strain of Paragraph 7, wherein the mutation is in a polypeptidecomprising a sequence having at least 25% identity to SEQ ID NO: 36 asdetermined through use of FASTA version 3.0t78 with the defaultparameters.

13. The strain of Paragraph 7 further comprising a mutation in a genethat inhibits the production of the autoinducer.

14. The strain of Paragraph 13, wherein the mutation is in a luxS gene.

15. The strain of Paragraph 14, wherein the mutation is in a nucleicacid comprising a sequence selected from the group consisting of SEQ IDNOs: 1-9.

16. The strain of Paragraph 13, wherein the mutation is in a nucleicacid comprising a sequence having at least 30% identity as determinedthrough use of BLASTN version 2.0 with the default parameters to asequence selected from the group consisting of SEQ ID NOs: 1-9.

17. The strain of Paragraph 13, further comprising a mutation thatinhibits the detection of a second autoinducer that is anacylho-moserine lactone.

18. The method of Paragraph 17, wherein the second autoinducer is anacyl-homoserine lactone.

19. The method of Paragraph 17, wherein the second autoinducer isN-(3-hydroxyacyl)-L-homoserine lactone and the acyl group comprises 4-12carbon atoms.

20. The method of Paragraph 19, wherein the acyl group comprises fourcarbon atoms.

21. The strain of Paragraph 17, wherein the mutation is in the luxNgene.

22. The strain of Paragraph 1, wherein the autoinducer is theautoinducer-2 produced by Vibrio harveyi.

23. The strain of Paragraph 1, wherein the autoinducer is apentanedione.

24. The strain of Paragraph 20, wherein the pentanedione is4,5-dihydroxy-2,3-pentanedione.

25. The strain of Paragraph 1, wherein the strain belongs to a speciesselected from the group consisting of S. typhimurium and E. coli.

26. The strain of Paragraph 1, wherein the strain belongs to a speciesselected from the group consisting of Haemophilus influenzae,Helicobacter pylori, Bacillus subtilis, Borrelia burgdorferi and Vibriocholerae.

27. The strain of Paragraph 1, wherein the strain is a strain of Vibrioharveyi.

28. A method for identifying a compound that modulates the response to afirst autoinducer that is not an acyl-homoserine lactone and that caninteract with the Vibrio harveyi LuxQ protein, thereby inducingexpression of a Vibrio harveyi operon comprising the luxCDABE genes,comprising:

obtaining a cell having increased expression of a transporter thattransports the autoinducer into the cell, wherein the cell produces adetectable signal in response to the first autoinducer;

measuring the response of the cell to the first autoinducer in thepresence and absence of a test compound; and

comparing the responses to determine whether the test compound modulatesthe response to the first autoinducer.

29. The method of Paragraph 28, wherein the cell has been geneticallyengineered to increase expression of the transporter.

30. The method of Paragraph 28, wherein the transporter comprises atleast one polypeptide comprising a sequence selected from the groupconsisting of SEQ ID NOs.: 37-40 and a sequence having at least 25%identity as determined through use of FASTA version 3.0t78 with thedefault parameters to one of SEQ ID NOs.: 37-40.

31. The method of Paragraph 28, wherein the transporter comprises acomplex comprising each of the amino acid sequences of SEQ ID NOs. 37-40or amino acid sequences having at least 25% identity as determinedthrough use of FASTA version 3.0t78 with the default parameters to eachof the sequences of SEQ ID NOs.: 37-40.

32. The method of Paragraph 29, wherein the cell comprises at least onevector from which one or more polypeptides included in the transporterare expressed.

33. The method of Paragraph 29, wherein the cell comprises a mutationthat increase expression of the transporter.

34. The method of Paragraph 33, wherein the mutation is in a geneencoding a repressor that reduces expression of the transporter.

35. The method of Paragraph 34 wherein the mutation is in a genecomprising the sequence of SEQ ID NO: 28.

36. The method of Paragraph 34, wherein the mutation is in a genecomprising a sequence having at least 30% identity to SEQ ID NO: 28 asdetermined through use of BLASTN version 2.0 with the defaultparameters.

37. The method of Paragraph 34, wherein the mutation is in a geneencoding a polypeptide comprising the sequence of SEQ ID NO: 36

38. The method of Paragraph 34, wherein the mutation is in a nucleicacid comprising a sequence that hybridizes to a probe comprising atleast 20 consecutive nucleotides of SEQ ID NO: 28 in 6×SSC at about 45°C. followed by one or more washes in 0.1×SDS at about 68° C.

39. The method of Paragraph 34, wherein the mutation is in a polypeptidecomprising a sequence having at least 25% identity to SEQ ID NO: 36 asdetermined through use of FASTA version 3.0t78 with the defaultparameters.

40. The method of Paragraph 34 wherein the cell further comprises amutation in a gene that inhibits the production of the autoinducer.

41. The method of Paragraph 40, wherein the mutation that inhibits theproduction of the autoinducer is in a luxS gene.

42. The method of Paragraph 41, wherein the mutation that inhibits theproduction of the autoinducer is in a nucleic acid comprising a sequenceselected from the group consisting of SEQ ID NOs: 1-9.

43. The method of Paragraph 40, wherein the mutation is in a nucleicacid comprising a sequence having at least 30% nucleotide identity asdetermined through use of BLASTN version 2.0 with the default parametersto a sequence selected from the group consisting of SEQ ID NOs: 1-9.

44. The method of Paragraph 40, wherein the cell further comprises amutation that inhibits the detection of a second autoinducer that is anacylhomoserine lactone.

45. The method of Paragraph 44, wherein the second autoinducer isN-(3-hydroxyacyl)-L-homoserine lactone and the acyl group comprises 4-12carbon atoms.

46. The method of Paragraph 45, wherein the acyl group comprises fourcarbon atoms.

47. The method of Paragraph 44, wherein the mutation that inhibits thedetection of the second autoinducer is in the luxN gene.

48. The method of Paragraph 28, wherein the autoinducer is theautoinducer-2 produced by Vibrio harveyi.

49. The method of Paragraph 28, wherein the autoinducer is apentanedione.

50. The method of Paragraph 49, wherein the pentanedione is4,5-dihydroxy-2,3-pentanedione.

51. The method of Paragraph 28, wherein the cell belongs to a speciesselected from the group consisting of S. typhimurium and E. coli.

52. The method of Paragraph 28, wherein the cell belongs to a speciesselected from the group consisting of Haemophilus influenzae,Helicobacter pylori, Bacillus subtilis, Borrelia burgdorferi and Vibriocholerae.

53. The method of Paragraph 1, wherein the cell is a Vibrio harveyicell.

54. A method for screening a candidate compound for the ability to bindto a transporter that transports an autoinducer into a cell, wherein theautoinducer is not an acyl-homoserine lactone and can interact with theVibrio harveyi LuxQ protein thereby inducing expression of a Vibrioharveyi operon comprising the luxCDABE genes, comprising:

contacting the transporter with the candidate compound; and

determining whether the compound specifically binds to the transporter.

55. The method of Paragraph 54, wherein the compound comprises adetectable label.

56. The method of Paragraph 54, wherein the transporter comprises atleast one polypeptide comprising an amino acid sequence selected fromthe group consisting of SEQ ID NOs.: 37-40 and a sequence having atleast 25% amino acid identity as determined through use of FASTA version3.0t78 with the default parameters to one of SEQ ID NOs.: 37-40.

57. The method of Paragraph 54, wherein the transporter comprises acomplex comprising each of the amino acid sequences of SEQ ID NOs. 37-40or amino acid sequences having at least 25% amino acid identity asdetermined through use of FASTA version 3.0t78 with the defaultparameters to each of the amino acid sequences of SEQ ID NOs.: 37-40.

58. A method of screening a candidate compound for the ability tomodulate the binding of an autoinducer to a transporter, wherein theautoinducer is not an acyl-homoserine lactone and can interact with theVibrio harveyi LuxQ protein thereby inducing expression of a Vibrioharveyi operon comprising the luxCDABE genes, comprising:

comparing the binding of the autoinducer to the transporter in thepresence and absence of the candidate compound; and

determining whether the the extent of binding of the autoinducer to thetransporter in the presence of the compound increases or decreasesrelative to the extent of binding in the absence of the compound.

59. A method of screening a candidate compound for the ability to bind apolypeptide comprising:

contacting a polypeptide comprising a sequence selected from the groupconsisting of SEQ ID NOs. 37-40 and a sequence having at least 25%identity as determined through use of FASTA version 3.0t78 with thedefault parameters to one of the sequences of SEQ ID NOs.: 37-40 withthe compound; and

determining whether the compound specifically binds to the polypeptide.

60. An isolated bacterial strain comprising a mutation that inhibits thetransport of an autoinducer that is not an acyl-homoserine lactone andthat can interact with the Vibrio harveyi LuxQ protein thereby inducingexpression of a Vibrio harveyi operon comprising the luxCDABE genes.

61. The bacterial strain of Paragraph 60, wherein the mutation is in agene selected from the group consisting of the lsrA, lsrB, lsrC, andlsrD genes.

62. The bacterial strain of Paragraph 61, wherein the strain is aSalmonella typhimurium strain.

63. The bacterial strain of Paragraph 62, wherein the mutation is in asequence selected from the group consisting of SEQ ID NOs.: 29-32.

64. The bacterial strain of Paragraph 63, wherein the mutation is in agene encoding a polypeptide comprising a sequence selected from thegroup consisting of SEQ ID NOs.: 37-40.

65. The bacterial strain of Paragraph 63, wherein the mutation is in anucleic acid comprising a sequence selected from the group consisting ofa sequence having at least 30% nucleotide identity to one of SEQ IDNOs.: 29-32 as determined through use of BLASTN version 2.0 with thedefault parameters.

66. A bacterial strain that overexpresses or underexpresses apolypeptide comprising a sequence selected from the group consisting ofSEQ ID NOs. 36-43 and a sequence having at least 25% identity to one ofSEQ ID NOs: 36-43 relative to a wildtype strain.

67. A bacterial strain that overexpresses or underexpresses apolypeptide comprising a sequence selected from the group consisting ofSEQ ID NOs. 36-43 and a sequence having at least 25% identity to one ofSEQ ID NOs: 36-43 relative to a wildtype strain.

68. An isolated or purified nucleic acid comprising a sequence selectedfrom the group consisting of SEQ ID NOs.: 28-35 and a fragmentcomprising at least 20 consecutive nucleotides of one of of SEQ ID NOs.:28-35.

69. An isolated or purified nucleic acid comprising a fragment of one ofSEQ ID NOs.: 28-35 that encodes a polypeptide that can facilitate thetransport of an autoinducer into a cell, wherein the autoinducer is notan acyl-homoserine lactone and can interact with the Vibrio harveyi LuxQprotein thereby inducing expression of a Vibrio harveyi operoncomprising the luxCDABE genes.

70. A recombinant vector comprising a sequence selected from the groupconsisting of SEQ ID NOs: 28-35 operably linked to a heterologouspromoter.

71. An isolated or purified protein comprising a sequence selected fromthe group consisting of SEQ ID NOs.: 36-43 and a fragment comprising atleast 10 consecutive amino acids of one of of SEQ ID NOs. 36-43.

72. An isolated or purified polypeptide comprising a fragment of one ofSEQ ID NOs.: 36-43 that encodes a polypeptide that can facilitate thetransport of an autoinducer into a cell, wherein the autoinducer is notan acyl-homoserine lactone and can interact with the Vibrio harveyi LuxQprotein thereby inducing expression of a Vibrio harveyi operoncomprising the luxCDABE genes.

73. An antibody that binds to a polypeptide selected from the groupconsisting of SEQ ID NOs.: 36-43.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

The present invention relates to the identification of genes andpolypeptide whose expression level is regulated by the autoinducer AI-2.AI-2 has been described in U.S. patent applications Ser. Nos.09/853,832, entitled Compounds and Methods for Regulating BacterialGrowth and Pathogenesis, filed May 10, 2001, U.S. Provisional PatentApplication Ser. No. 60/203,000 entitled Compounds and Methods forRegulating Bacterial Growth and Pathogenesis filed May 10, 2000, U.S.Provisional Patent Application Ser. No. 60/254,398, entitled Compositionand Methods for Regulating Bacterial Growth and Pathogenesis, filed Dec.7, 2000 and U.S. patent application Ser. No. 09/453,976, entitledCompositions and Methods for Regulating Bacterial Pathogenesis, filedDec. 2, 1999, the disclosures of which are incorporated herein byreference in their entireties. As discussed briefly above, a variety ofbacterial species, some of them mammalian pathogens, secrete an organicsignaling compound that stimulates the expression of luminescence in V.harveyi. The compound secreted by these organisms mimics V. harveyi AI-2in its physical and functional features. The production in bacteria ofthis novel signaling compound is regulated by changes in environmentalconditions associated with a shift from a free-living existence to acolonizing or pathogenic existence in a host organism. Thus, in additionto stimulating luminescence genes (specifically luxCDABE) through itsinteraction with the luxQ protein in V. harveyi, the signaling compoundis expected to stimulate a variety of pathogenesis related genes in thebacterial species that produce it.

The signaling factor is produced by a variety of bacteria, including butnot limited to: Vibrio harveyi, Vibrio cholerae, Vibrioparahaemolyticus, Vibrio alginolyticus, Pseudomonas phosphoreum,Yersinia enterocolitica, Escherichia coli, Salmonella typhimurium,Haemophilus influenzae, Helicobacter pylori, Bacillus subtilis, Borreliaburgfdorferi, Neisseria meningitidis, Neisseria gonorrhoeae, Yersiniapestis, Campylobacter jejuni, Deinococcus radiodurans, Mycobacteriumtuberculosis, Enterococcus faecalis, Streptococcus pneumoniae,Streptococcus pyogenes and Staphylococcus aureus.

In a genetic screen for functions regulated by AI-2 in S. typhimurium,we identified an operon predicted to encode an ABC transporter withsimilarity to the ribose transporter of E. coli and S. typhimurium (FIG.17). This operon (the lsr operon, SEQ ID NO: 44) is induced in thepresence of luxS and AI-2 (FIG. 19), and AI-2 regulation of lsr operonexpression requires the LsrR DNA binding regulatory protein (FIG. 20 andFIGS. 22 and 23). The function of the Lsr transporter is to import AI-2from the external environment because strains possessing mutations inthe Lsr transporter do not remove AI-2 from the culture medium, whereasAI-2 disappears from culture fluids of S. typhimurium strains possessinga wild type Lsr transporter. Additionally, strains derepressed for lsrexpression by inactivation of lsrR remove AI-2 more rapidly than wildtype (FIG. 24). In earlier work we showed that accumulation of AI-2 byS. typhimurium is maximal in late exponential phase, and all the AI-2activity disappears from the medium by the time stationary phase isreached (Surette and Bassler, 1998). Thus, the Lsr transporter isinvolved in AI-2 removal.

FIG. 25 shows a model for the function of the Lsr transporter and itsregulation by AI-2 and LsrR. LuxS synthesizes AI-2 in the cytoplasm.AI-2 is released to the external environment by an unknown mechanism.Extracellular AI-2 signals to the LsrR protein, again, by an unknownmechanism. In FIG. 25 we suggest that a sensor exists that isresponsible for detection of extracellular AI-2 and signal transductionto LsrR. Other possibilities exist, and are discussed herein. In theabsence of AI-2, LsrR acts to repress transcription of the lsr operon,most likely by binding at the lsr operon promoter analogous to RbsRbinding at the rbs promoter (Mauzy and Hermodson, 1992). AI-2 signallingto LsrR alleviates LsrR repression of the lsr operon, resulting intranscription of the genes encoding the Lsr ABC transport apparatus. TheLsr transporter, in turn, imports AI-2 from the extracellularenvironment into the cells. We do not know what becomes of the AI-2following import.

Two main types of ABC transporters exist in bacteria. One type of ABCtransporters consists of binding protein-dependent transporters thatfunction to import small molecules into the cell (Boos and Lucht, 1996;Holland and Blight, 1999; Nikaido and Hall, 1998). The Lsr transporterhas the highest homology to this class of ABC transporters, whosemembers include the RbsACB ribose transporter, the MglBAC galactosetransporter, and the HisJQMP histidine transporter (Boos and Lucht,1996). The second class of ABC transporters functions to exportcompounds out of the cell. These transporters do not require aperiplasmic binding protein, and their ligands vary greatly in size andcomposition (Boos and Lucht, 1996). The LmrA multidrug resistancetransporter, the HlyB hemolysin transporter of E. coli, and the ComABand SapTE oligopeptide autoinducer transporters of Streptococcuspneumoniae and Lactobacillus sake are examples of this second type ofABC exporter (Holland and Blight, 1999; Kleerebezem et al., 1997).Additionally, ABC transporters are employed for the transport ofcompounds in higher organisms, including humans. Deficiency in thefunction of ABC transporters has been implicated in many human diseases,the most well studied example being the CFTR chloride ion transporterthat is nonfunctional in cystic fibrosis patients (Holland and Blight,1999).

The homology between the Lsr complex and the family of ABC transporterssuggests a role for the Lsr complex in the transport of a ligand.Furthermore, because AI-2 is a ribose derivative, because the Lsrtransporter most closely resembles the ribose transporter, and becauseour evidence shows that the lsr genes are required for removal of AI-2from the external environment, we demonstrate that AI-2 is the ligandfor the Lsr transporter. These findings, coupled with the facts that theLsr transporter most closely resembles the importer type of ABCtransporter and that the Lsr complex is not required for export of AI-2,lead us to the conclusion that the Lsr complex transports AI-2 into thecell. However, it remains possible that the Lsr complex is required forthe modification or degradation of AI-2 on the cell surface.

We have shown previously that a secreted enzyme is not responsible forelimination of AI-2 from the medium because AI-2 is stable for longperiods of time in S. typhimurium cell-free spent culture fluids(Surette and Bassler, 1999). We have also observed that AI-2 does notdisappear from the supernatants of dead cells (not shown). These resultstogether indicate that elimination of AI-2 occurs either at the surfaceof living cells, or more likely, based on the findings in this report,disappearance of AI-2 is mediated by its transport into the cell via theLsr complex. However, at least one other Lsr independent mechanism forAI-2 elimination must exist in S. typhimurium because in both wild typeand lsrA, lsrB and lsrC mutant strains, although AI-2 activity does notdecrease during the first hour of incubation, the AI-2 activitydecreases in culture fluids after longer periods of incubation (20 h)(data not shown).

The mechanism of AI-2 signalling to LsrR to derepress transcription ofthe lsr operon can be from the inside or the outside of the cell. IfAI-2 acts from the inside, then AI-2 must enter the cells by somemechanism that is not dependent on the Lsr transporter. We conclude thisbecause S. typhimurium strains harboring mutations in the lsr operon,while deficient in the process of internalization of AI-2, remaincapable of AI-2-dependent derepression of transcription of the lsroperon. Therefore, if AI-2 is required to enter the cell to signal toLsrR, it does not require the Lsr apparatus, and furthermore, only aminor amount of AI-2 internalization can be required for the signallingprocess. We say this because we cannot detect any disappearance of AI-2from culture fluids prepared from strains containing mutations in thelsr transport genes. The alternative possibility is that AI-2 signals toLsrR from outside of the cell. Conceivably, an AI-2 sensor exists thatdetects external AI-2 and initiates a signalling cascade that culminatesin LsrR-mediated derepression of the transcription of the lsr operon. Wefavor an external mechanism for AI-2 signal relay to LsrR because it ismore consistent with our results. Specifically, regulation oftranscription of the lsr operon can occur in the absence of a detectablelevel of internalization of AI-2. FIG. 25 includes a putative AI-2sensor. Because LsrR contains a predicted helix-turn-helix DNA bindingdomain, and because in bacteria, genes specifying regulatory proteinsare frequently located adjacent to the promoter at which they bind, LsrRmay repress transcription of the lsr operon by binding at the lsrpromoter.

Evidence that the ligand for the Lsr complex is AI-2 includes findingsthat the Lsr transporter resembles the ribose transporter, because AI-2is derived from, and has structural similarity to ribose, and because ofthe transport data shown in FIG. 24. Consistent with this idea, the LuxPprotein in V. harveyi is the primary receptor for AI-2. The LuxP-AI-2complex initiates the quorum sensing signalling cascade (Bassler et al.,1994a). LuxP is a periplasmic protein homologous to the ribose bindingprotein RbsB, and to LsrB, the ribose binding protein homologue weidentified in the present work. We suggest that LsrB is the AI-2 bindingprotein in S. typhimurium. In this case, instead of initiating asignalling cascade, the function of LsrB is to bring AI-2 in contactwith the membrane bound components of the Lsr apparatus for transportinto the cell.

We do not yet fully understand the benefit that S. typhimurium derivesfrom synthesizing and releasing AI-2 only to internalize it at latertimes. One possibility is that AI-2 is initially used as a signal, then,at subsequent times, when AI-2 is no longer required for signaltransduction, S. typhimurium internalizes it for use as a carbon source.To test this idea, we attempted to grow wild type S. typhimurium on invitro prepared AI-2 as a sole carbon source. We found that S.typhimurium could not grow on AI-2, suggesting that S. typhimurium doesnot use AI-2 as a carbon source (not shown). Therefore, growth on AI-2cannot account for its disappearance from the medium. A secondpossibility is that the removal of AI-2 activity is required for itsmodification to another signal. For example, the LsrE epimerase, oranother enzyme, could convert AI-2 into an internal signal. Finally,AI-2 could be internalized for degradation. In this case, elimination ofAI-2 could serve to terminate the signalling process. Signal productioncoupled to subsequent elimination could allow S. typhimurium theflexibility to transition between several modes of existence. Forexample, as AI-2 is associated with the presence of many species ofbacteria, high levels of AI-2 could be indicative of the transition fromoutside a host to the intestinal environment, whereas low levels of AI-2could signal S. typhimurium that it has exited the intestinal tract forthe next location in the infection (i.e., the macrophage) where S.typhimurium is not in association with high numbers of commensalbacteria. Many possibilities exist, the point being that accumulationand disappearance of AI-2 could each initiate a different series ofbehavioral changes in S. typhimurium.

The genetic screen that led to the identification of the lsr operon wasdesigned to reveal the entire collection of genes regulated by AI-2.However, this experiment only yielded the lsr operon and metE. Forreasons discussed above, we do not believe that metE is a genuine targetof AI-2 regulation. It is possible that the sole target of AI-2regulation in S. typhimurium is the lsr operon. Alternatively, we favorthe idea that some bias in our screen exists that only allowed us toidentify the lsr operon. It is possible that lsr is the only exclusivetarget of AI-2. Other AI-2 targets could exist, but their regulation mayrequire AI-2 to act in conjunction with another signal(s). Under theconditions we perform our experiments, it is possible that we are notsupplying this additional hypothetical signal. Alternatively, two S.typhimurium quorum sensing signals could exist, either of which issufficient to regulate other target genes. Precedent for redundantsignalling factors involving AI-2 exists. In the V. harveyi quorumsensing circuit in which AI-2 was originally discovered, twoautoinducers (AI-1 and AI-2) operate in parallel to regulate theexpression of bioluminescence. Inactivation of genes involved in eithersignalling system alone does not abolish density-dependent expression ofluminescence in V. harveyi (Bassler et al., 1993; Bassler et al., 1994a;b). Moreover, nearly all Luxl/LuxR quorum sensing systems have now beenshown to be controlled by multiple autoinducers, and in many cases,intricate hierarchies of regulation exist in these systems (de Kievitand Iglewski, 2000; Miller and Bassler, 2001). The architecture of theS. typhimurium quorum sensing circuit could resemble that of V. harveyior other quorum sensing bacteria in that a complex and/or a redundantsignalling circuit could govern the process. Finally, it is possiblethat additional targets of AI-2 are only regulated when S. typhimuriumis grown in mixed-species consortium. We believe that AI-2 is a signalused by many species of bacteria for inter-species cell-cellcommunication. We assume that inter-species communication is a complexphenomenon that involves multiple sensory inputs. Therefore, AI-2 plusadditional signals, cell-cell contact and/or some other stimulusprovided by other species of bacteria could be required for S.typhimurium to react.

Discovery of LsrB, LsrR, LsrE epimerase, LsrC, lsrD channel components,and lsrA transporter ATPase suggests their use as drug targets fordevelopment of antibacterial agents. Each of these species can be usedin screening for inhibitors of autoinducer-2 binding or response, andspecifically to find compounds that inhibit binding of autoinducer-2 tothe species and/or block autoinducer-2 mediated responses, such as geneexpression. Using methods well-known to those of ordinary skill in theart, one can screen one or more compound libraries against each or anyof the above-mentioned targets to find which members of the libraryinteract with the target in the desired fashion. Typically suchinteraction inhibits the physiological function of the target; forexample, for an enzyme, such as lsrE epimerase, inhibits its catalysisof the reaction with which it is usually associated.

Methods of screening such libraries generally entail construction of anassay that measures binding to or inhibition of the target. For example,members of the library can be tagged with a fluorescent, radioactive, orother label, and their affinity for binding to the target can beassessed. Alternatively, the ability of library members to alter thecatalytic activity of an enzymatic target can be measured. Suchscreening methods are widely used, and hence are familiar to thoseskilled in drug discovery. Examples of such screens are described inU.S. Pat. Nos. 5,684,711, 6,046,002, 5,998,159 and 5,824,485, 6,455,263,6434490, 6,245,937, 6,207,861, and 6,054,047, 6,001,579, 5,721,099 thedisclosures of which are incorporated herein by reference in theirentireties. Other methods are disclosed in PCT publications No.WO9935494, WO9819162, WO9954728, the disclosures of which areincorporated herein by reference in their entireties., each of which ishereby incorporated by reference in its entirety.

Thus, in the present invention, strains carrying transposon insertionsin genes whose expression was reduced in luxS null strains relative towildtype strains (i.e. strains having insertions in genes that exhibitedelevated expression levels in the presence of the signaling factor) wereidentified in a screen. Among the identified strains were strainscarrying insertions in some of the genes encoding a transporter involvedin transporting the signaling factor into the cell. The proteins thatmake up the transporter are encoded by the lsrA, lsrB, lsrC and lsrDgenes that comprise SEQ ID NO. 29, SEQ ID NO: 32, SEQ ID NO: 30, and SEQID NO: 31 respectively and that encode the LsrA, LsrB, LsrC and LsrDproteins comprising SEQ ID NO 37, SEQ ID NO: 40, SEQ ID NO: 38, and SEQID NO: 39 respectively. In particular, strains carrying insertions inthe lsrA, lsrB and lsrC genes were identified in the screen. Otherstrains identified in the screen were found to carry insertions in thelsrE and lsrF genes (SEQ ID NO: 35 and SEQ ID NO: 33 respectively,encoded the LsrE and LsrF proteins of SEQ ID NO: 43 and SEQ ID NO: 41respectively). . The lsrA, lsrB, lsrC, lsrD, lsrE, lsrF, and lsrG geneslie in an operon that the LsrR repressor regulates (the lsrR genecomprises SEQ ID NO: 28 and the LsrR protein has SEQ ID NO: 36). ThelsrE, lsrF, lsrG and lsrR genes comprise SEQ ID NO: 35, SEQ ID NO: 33,SEQ ID NO: 34 and SEQ ID NO: 28 respectively that encode proteinscomprising SEQ ID NO: 43, SEQ ID NO:41, SEQ ID NO:42 and 36respectively.

One aspect of the present invention is an isolated or purified nucleicacid comprising one of SEQ ID NOs: 28-35, a nucleic acid homologous toone of SEQ ID NOs: 28-35, fragments comprising at least 20, at least 30,at least 40, at least 50, at least 60, at least 70, at least 80, atleast 100, at least 150, at least 200 or more than 200 consecutivenucleotides of one of SEQ ID NOs.: 28-35, fragments comprising at least20, at least 30, at least 40, at least 50, at least 60, at least 70, atleast 80, at least 100, at least 150, at least 200 or more than 200consecutive nucleotides of a nucleic acid homologous to one of SEQ IDNOs.: 28-35, or a nucleic acid complementary to any of the foregoing. Ina preferred embodiment, the isolated or purified nucleic acid comprisingone of SEQ ID NOs.: 28-35, a nucleic acid homologous thereto, or afragment thereof is inserted into a vector. In some embodiments, thevector is not included in a genomic library that contains a large numberof vectors most of which contain a nucleic acid other than one of SEQ IDNOs.: 28-35, a nucleic acid homologous thereto, or a fragment thereofinserted therein. Thus, in a preferred embodiment, the nucleic acid ofone of SEQ ID NOs.: 28-35, a nucleic acid homologous thereto, or afragment thereof represents at least 90%, at least 80%, at least 70%, atleast 60%, at least 50%, at least 40%, or at least 30%, of the nucleicacid inserts in the vector.

In a further preferred embodiment, the insert in the vector does notcontain a substantial amount of genomic DNA that is naturally adjacentto the nucleic acid of one of SEQ ID NOs.: 28-35, a nucleic acidhomologous thereto, or a fragment thereof or that is naturally adjacentto the operon in which the one of SEQ ID NOs.: 28-35, a nucleic acidhomologous thereto, or fragment thereof lies. Preferably, in thisembodiment, the insert in the vector encodes one or more of thepolypeptides of SEQ ID NOs.: 36-43 but does not encode a polypeptideother than the foregoing.

The nucleic acid that is homologous to one of one of SEQ ID NOs.: 28-35may have at least 97%, at least 95%, at least 90%, at least 85%, atleast 80%, at least 70%, at least 60%, at least 50%, at least 40%, atleast 30%, or at least 20% sequence identity to a sequence selected fromthe group consisting of SEQ ID NOS.: 28-35 or the sequence complementarythereto. Identity may be measured using BLASTN version 2.0 with thedefault parameters or tBLASTX with the default parameters. (Altschul, S.F. et al. Gapped BLAST and PSI-BLAST: A New Generation of ProteinDatabase Search Programs, Nucleic Acid Res. 25: 3389-3402 (1997), thedisclosure of which is incorporated herein by reference in its entirety)Alternatively a homologuous nucleic acid could be identified bymembership of the gene of interest to a functional orthologue cluster.All other members of that orthologue cluster would be consideredhomologues. Such a library of functional orthologue clusters can befound at http://www.ncbi.nlm.nih.gov/COG. A gene can be classified intoa cluster of orthologous groups or COG by using the COGNITOR programavailable at the above web site, or by direct BLASTP comparison of thegene of interest to the members of the COGs and analysis of theseresults as described by Tatusov, R. L., Galperin, M. Y., Natale, D. A.and Koonin, E. V. (2000) The COG database: a tool for genome-scaleanalysis of protein functions and evolution. Nucleic Acids Research v.28 n. 1, pp 33-36.

The homologous nucleic acid may also comprise sequences that encodepolypeptides having at least 99%, 95%, at least 90%, at least 85%, atleast 80%, at least 70%, at least 60%, at least 50%, at least 40% or atleast 25% maino acid identity or similarity to a polypeptide comprisingthe sequence of one of SEQ ID NOs:36-43 or fragments comprising at least5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive aminoacids thereof as determined using the FASTA version 3.0t78 algorithmwith the default parameters. Alternatively, protein identity orsimilarity may be identified using BLASTP with the default parameters,BLASTX with the default parameters, TBLASTN with the default parameters,or tBLASTX with the default parameters. (Altschul, S. F. et al. GappedBLAST and PSI-BLAST: A New Generation of Protein Database SearchPrograms, Nucleic Acid Res. 25: 3389-3402 (1997), the disclosure ofwhich is incorporated herein by reference in its entirety).

The homologous nucleic acid may also be a nucleic acid that hybridizesunder stringent conditions to a nucleic acid selected from the groupconsisting of the sequences complementary to one of SEQ ID NOS.: 28-35and nucleic acids comprising sequences that hybridize under stringentconditions to a fragment comprising at least 10, 15, 20, 25, 30, 35, 40,50, 75, 100, 150, 200, 300, 400, or 500 consecutive nucleotides of thesequences complementary to one of SEQ ID NOS.: 28-35. As used herein,“stringent conditions” means hybridization to filter-bound nucleic acidin 6×SSC at about 45° C. followed by one or more washes in 0.1×SSC/0.2%SDS at about 68° C. Other exemplary stringent conditions may refer,e.g., to washing in 6×SSC/0.05% sodium pyrophosphate at 37° C., 48° C.,55° C., and 60° C. as appropriate for the particular probe being used.

The homologous nucleic acid may also be a nucleic acid comprising asequence that hybridizes under moderate conditions to a sequenceselected from the group consisting of the sequences complementary to oneof SEQ ID NOS 28-35 and nucleic acids comprising sequences thathybridize under moderate conditions to a fragment comprising at least10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500consecutive nucleotides of the sequences complementary to one of SEQ IDNOS.: 28-35. As used herein, “moderate conditions” means hybridizationto filter-bound DNA in 6× sodium chloride/sodium citrate (SSC) at about45° C. followed by one or more washes in 0.2×SSC/0.1% SDS at about42-65° C.

The homologous nucleic acids may also be a nucleic acid comprising asequence that encodes a gene product whose activity may be complementedby one of the polypeptides of SEQ ID NOs. 36-43. In some embodiments,the homologous nucleic acid may encode a gene product whose activity iscomplemented by the gene product encoded by a nucleic acid comprising asequence selected from the group consisting of SEQ ID NOS.: 28-35.

Nucleic acids homologous to the luxS nucleic acids of SEQ ID NOs.: 1-9or the luxN nucleic acid of SEQ ID NO: 57 have the same relationships tothe reference sequences of SEQ ID NOs. :1-9 and SEQ ID NO: 57 as theabove-described nucleic acids homologous to SEQ ID NOs. 28-35 have tothe reference sequences of SEQ ID NOs. 28-35.

Another embodiment of the present invention is an isolated or purifiedpolypeptide comprising one of SEQ ID NOs. 36-43, a polypeptidehomologous thereto, or a fragment comprising at least 10, at least 20,at least 30, at least 40, at least 50, at least 60, at least 70, atleast 80, at least 90, at least 100, or more than one consecutive aminoacids thereof. The homologous polypeptide may have at least 99%, 95%, atleast 90%, at least 85%, at least 80%, at least 70%, at least 60%, atleast 50%, at least 40% or at least 25% amino acid identity orsimilarity to a polypeptide comprising one of SEQ ID NOs.: 36-43, orpolypeptides having at least 99%, 95%, at least 90%, at least 85%, atleast 80%, at least 70%, at least 60%, at least 50%, at least 40% or atleast 25% amino acid identity or similarity to a to a fragmentcomprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150consecutive amino acid of a polypeptide comprising one of SEQ ID NOs.:36-43. Identity or similarity may be determined using the FASTA version3.0t78 algorithm with the default parameters. Alternatively, proteinidentity or similarity may be identified using BLASTP with the defaultparameters, BLASTX with the default parameters, or TBLASTN with thedefault parameters. (Altschul, S. F. et al. Gapped BLAST and PSI-BLAST:A New Generation of Protein Database Search Programs, Nucleic Acid Res.25: 3389-3402 (1997), the disclosure of which in incorporated herein byreference in its entirety).

Polypeptides homologous to the luxS polypeptides of SEQ ID NOs.: 10-70or the luxN polypeptide of SEQ ID NO: 58 have the same relationships tothe reference sequences of SEQ ID NOs. :10-17 and SEQ ID NO: 58 as theabove-described nucleic acids homologous to SEQ ID NOs. 36-43 have tothe reference sequences of SEQ ID NOs. 36-43.

Another embodiment of the present invention is an isolated bacterialstrain having an increased or decreased transcription level of a nucleicacid comprising one of SEQ ID NOs.: 28-35 or an increased or decreasedexpression level of a polypeptide comprising one of SEQ ID NOs: 36-43relative to a wild type strain. In a preferred aspect of thisembodiment, the strain overexpresses or underexpresses a transporterthat transports an autoinducer into the cell. Preferably, theautoinducer is not an acyl-homoserine lactone and is able to interactwith the Vibrio harveyi luxQ protein, thereby inducing expression of aVibrio harveyi operon comprising the luxCDABE genes. In a preferredembodiment the autoinducer is AI-2 from Vibrio harveyi or thecorresponding autoinducer from another organism.

The strain may be obtained using genetic engineering techniques familiarto those skilled in the art. For example, strains that have an increasedexpression level of the transporter may be obtained by introducing avector in which one or more genes encoding one or more polypeptidesmaking up the transporter are under the control of a promoter thatprovides a level of transcription resulting in elevated expression ofthe transporter relative to a wild type cell into a cell. In someembodiments, an operon comprising the lsrA, lsrB, lsrC and lsrD genes orgenes encoding proteins homologous thereto may be placed under thecontrol of the promoter.

Strains that have a decreased expression level of the transporterrelative to a wild type cell may also be obtained using geneticengineering. For example, the strains may be obtained by introducing avector that directs the transcription of a ribozyme that cleaves a RNAencoding one or more genes encoding one or more polypeptides making upthe transporter into a cell. Alternatively, strains that have adecreased expression level of the transporter relative to a wild typecell may be obtained by overexpressing the lsrR repressor protein or aprotein homologous thereto in the cell. Such strains may be useful, forexample, for evaluating whether AI-2 has any cellular effects in theabsence of its transport into the cell.

In some embodiments, the strains that overexpress or underexpress thetransporter relative to a wild type cell may possess a mutation that isresponsible for the overexpression or underexpression of thetransporter. For example, strains that overexpress the transporter mayhave a mutation in the lsrR gene that reduces the level of repression ofthe lsr operon by the lsrR protein or a mutation in the promoter fromwhich the lsr operon is transcribed that increases the strength of thepromoter. Such strains will have an increased transcription level of themRNA encoding the LsrA, LsrB, lsrC and lsrD proteins that make up thetransporter relative to a wild type cell. Strains that underexpress thetransporter may have a mutation in the lsrR gene that increases thelevel of repression of the lsr operon by the lsrR protein or may have amutation in the promoter from which the lsr operon is transcribes thatreduces the level of transcription therefrom.

The mutation that causes overexpression or underexpression of thetransporter may be generated via chemical mutagenesis techniques,transpon mediated mutagenesis techniques, including methods such asthose described herein, site directed mutagenesis techniques, or othermethods familiar to those skilled in the art. Alternatively, strainscontaining the mutation may be isolated from naturally occurringpopulations.

Another aspect of the present invention is a method for screening a testcompound for the ability to modulate the response to an autoinducer.Preferably, the autoinducer in not an acyl-homoserine lactone and isable to interact with the Vibrio harveyi luxQ protein, thereby inducingexpression of a Vibrio harveyi operon comprising the luxCDABE genes. Ina preferred embodiment the autoinducer is AI-2. In some embodiments, theautoinducer may be AI-2 from Vibrio harveyi or the correspondingautoinducer from another organism.

Cells that produce a detectable response to the autoinducer and thathave an increased expression level of an autoinducer that transports theautoinducer into the cell are contacted with the autoinducer. Theresponses of the cells to the autoinducer in the presence and absence ofthe test compound are measured and compared to identify compounds thatmodulate the response to the autoinducer.

The cell may be from any desired species that produces a detectablesignal in response to the autoinducer or a cell that has been engineeredto produce a detectable signal in response to the autoinducer. In someembodiments, the cell is a Salmonella typhimurium cell. For example, insome embodiments, the cell may be a Salmonella typhimurium cell carryinga mutation in the lsrR gene that causes the transporter to be expressedat a higher level than it is expressed in wild type cells.Alternatively, in some embodiments, the cell is from a species otherthan Salmonella typhimurium and carries a mutation in a gene encoding apolypeptide homologous to the lsrR polypeptide that causes thetransporter to be expressed at a level higher than it is expressed inwild type cell.

In other embodiments, the cell may be a Vibrio harveyi, E. coli,Haemophilus, influenza, Helicobacter pylori, Bacillus subtilis, Borreliaburdorferi or Vibrio cholerae cell. In some embodiments, the cell maycarry a mutation in a gene encoding a protein homologous to the lsrRprotein of Salmonella typhimurium that causes the expression level ofthe transporter to be higher than that of a wild type cell.

The cell may produce any detectable signal in response to theautoinducer. For example, in some embodiments, the cell producesbioluminescence in response to the autoinducer. Thus, in someembodiments, the cell is a Vibrio harveyi cell that producesbioluminescence in response to the autoinducer via induction of theluxCDABE operon.

Alternatively, in some embodiments, the detectable signal may beinduction of mRNA transcription or protein expression in response to theautoinducer. Induction of mRNA transcription may be measured with any ofa variety of techniques familiar to those skilled in the art, includingNorthern analysis or detection of the transcript through use of nucleicacid amplification techniques such as PCR. Induction of proteinexpression may also be measured with any of a variety of techniquesfamiliar to those skilled in the art including gel electrophoresis,Western blotting, or enzymatic activity assays. For example, in someembodiments, the cell may be genetically engineered to express a markerprotein such as β-galactosidase, chloramphenicol acetyltransferase,β-glucuronidase, luciferase or green fluorescent protein in response tothe autoinducer. Thus, in some embodiments, a nucleic acid encoding themarker protein may be operably linked to the promoter from the lsroperon or to the luxCDABE promoter and introduced into the cell suchthat expression of the marker protein is induced by the autoinducer.Alternatively, in other embodiments, an autoinducer responsive promoterother than the lsr or luxCDABE promoter may be operably linked to anucleic acid encoding the marker protein. The the autoinducer responsivepromoter may be from the same species as the cell to be used in themethod or, alternatively, the the autoinducer responsive promoter may befrom a heterologous organism.

In some embodiments, the cell may be a Salmonella typhimurium cell inwhich the expression of lacZ is regulated by AI-2, such as the cellscarrying mudJ insertions described herein.

In some embodiments, in addition to expressing the transporter at ahigher level than wild type cells, the cell that produces a detectablesignal in response to the autoinducer has a genetic alteration thatinhibits production of the autoinducer. In some embodiments, the geneticalteration is introduced into the cell through use of such geneticengineering techniques as site directed mutagenesis, insertionalmutagenesis, or chemical mutagenesis followed by appropriate selection.Alternatively, cells containing the genetic alteration may be isolatedor selected from a natural population.

In some embodiments, the genetic alteration that inhibits production ofthe autoinducer is in the Vibrio harveyi luxS gene, a gene havinghomology to the Vibrio harveyi luxS gene, or a gene encoding apolypeptide having homology to the Vibrio harveyi luxS polypeptide. Forexample, the genetic alteration may be in a gene having a sequence withat least 50%, at least 60%, or at least 80% sequence homology to theVibrio harveyi luxS gene. In other embodiments the genetic alteration isin a gene encoding a polypeptide having at least 57% or at least 85%homology to the Vibrio harveyi luxS polypeptide. In still furtherembodiments, the genetic alteration is in a gene encoding a polypeptidehaving at least 32%, at least 45%, at least 74% or at least 80% sequenceidentity to the Vibrio harveyi luxS polypeptide.

In some embodiments, in addition to expressing the transporter at alevel higher than wild type cells, the cells have a first geneticalteration that inhibits production of an autoinducer that is not anacyl-homoserine lactone and a second genetic alteration that inhibitsdetection or response to another autoinducer that is an acyl-homoserinelactone. For example, in some embodiments, the cell may be a Salmonellatyphimurium cell having a mutation in the lsrR gene of SEQ ID NO: 28,the luxS gene comprising SEQ ID NO: 4 and a gene homologous to theVibrio harveyi luxN gene. In other embodiments, the cells is a Vibrioharveyi cell with a mutation in a gene encoding a polypeptide homologousto the lsrR polypeptide of SEQ ID NO. 36, the first genetic alterationis in the luxS gene and the second genetic alteration is in the luxNgene. Thus, in some embodiments, the cell may be a Vibrio harveyi MM32cell as described herein. However, the first and second geneticalterations may be in any gene that provides the phenotypes discussedabove, including the genes discussed above, and the cell may be from anysuitable species, including the species specifically enumerated herein.

The response of the cell to the autoinducer is measured in the presenceand absence of a test compound. The test compound may benaturally-occuring, such as a compound from a natural products library,or may be of synthetic origin, such as a compound generated through useof combinatorial chemistry.

The response of the cell to the autoinducer in the presence and absenceof the test compound is compared. In some embodiments, the test compoundalters the response to the autoinducer at least two fold, at least 10fold, at least 20 fold, at least 50 fold, at least 100 fold, at least1000 fold, or even more than 1000 fold.

Another embodiment of the present invention is a method for screening acandidate compound for the ability to bind to a polypeptide comprisingthe sequence of one of SEQ ID NOs.: 36-43 or a fragment thereof, apolypeptide comprising a sequence homologous to the sequence of one ofSEQ ID NOs.: 36-43 or a fragment thereof, a transporter that transportsan autoinducer into a cell or to one of the polypeptides that make upthe transporter. Preferably, the autoinducer is not an acyl-homoserinelactone and is able to interact with the Vibrio harveyi luxQ protein,thereby inducing expression of a Vibrio harveyi operon comprising theluxCDABE genes. In a preferred embodiment the autoinducer is AI-2 fromVibrio harveyi or the corresponding autoinducer from another organism.

The candidate compound may be from any source, including chemicallibraries generated using combinatorial chemistry or natural productlibraries. U.S. Pat. Nos. 5,463,564 and 5,574,656, to Agrafiotis, etal., entitled “System and Method of Automatically Generating ChemicalCompounds with Desired Properties,” the disclosures of which areincorporated herein by reference in their entireties, disclose methodsfor generating libraries of compounds. Preferably, the candidatecompound is labeled with a detectable label such as a radioactive orfluorescent moeity. Alternatively, the compound may be detectable usinga labeled antibody.

The candidate compound is placed in contact with the polypeptidecomprising the sequence of one of SEQ ID NOs.: 36-43 or a fragmentthereof, a polypeptide comprising a sequence homologous to the sequenceof one of SEQ ID NOs.: 36-43 or a fragment thereof, a transporter or apolypeptide that makes up the transporter under conditions thatfacilitate the binding of the compound to the transporter orpolypeptide. A washing step is then performed under conditions thatwould remove nonspecifically bound compound. The amount of compoundbound to the transporter or polypeptide is then measured to determinewhether the compound specifically binds to the transporter orpolypeptide.

The transporter or polypeptide may be fixed to a solid support such as amicrotiter plate or bead or, alternatively, may be present in a membraneor vesicle. Methods for attaching the transporter or polypeptide to suchsolid supports and methods for preparing membranes or vesiclescontaining the transporter or polypeptide are familiar to those skilledin the art.

Methods for screening compounds for desired structural, binding, andfunctional properties are disclosed in U.S. Pat. Nos. 5,684,711,6,046,002, 5,998,159 and 5,824,485, 6,455,263, 6,434,490, 6,245,937,6,207,861, and 6,054,047, 6,001,579, 5,721,099 the disclosures of whichare incorporated herein by reference in their entireties. Other methodsare disclosed in PCT publications No. WO9935494, WO9819162, WO9954728,the disclosures of which are incorporated herein by reference in theirentireties.

A further aspect of the present invention is a method for screening acandidate compound for the ability to modulate the binding of anautoinducer to a transporter. Preferably, the autoinducer is not anacyl-homoserine lactone and is able to interact with the Vibrio harveyiluxQ protein, thereby inducing expression of a Vibrio harveyi operoncomprising the luxCDABE genes. In a preferred embodiment the autoinduceris AI-2. In some embodiments, the autoinducer may be AI-2 from Vibrioharveyi or the corresponding autoinducer from another organism.

In the foregoing method, the extent of binding of the autoinducer to thetransporter is compared in the presence and absence of the candidatecompound to determine whether the extent of binding of the autoinducerto the transporter in the presence of the candidate compound issignificantly increased or decreased relative to the extent of bindingin the absence of the candidate compound.

In one embodiment, the extent of binding of the autoinducer to thetransporter is measured by contacting a cell expressing the transporter(such as a cell that expresses the transporter at a level higher than awild type cell) with a solution containing the autoinducer in thepresence or absence of the compound. After a sufficient amount of timehas elapsed, the solution is removed from the cells and placed incontact with cells that produce a detectable response to theautoinducer, such as those described herein. If the compound inhibitsthe transport of the autoinducer into the cell, then the solution fromcells contacted with the compound will contain a significantly higheramount of the autoinducer than the solution from cells that were notcontacted with the compound. Thus, the level of the detectable responseto the autoinducer will be greater in cells contacted with the solutionfrom cells contacted with the compound than the level of detectableresponse in cells contacted with the solution from cells that were notcontacted with the compound. If the compound increases the transport ofthe autoinducer into the cell, the level of the detectable response tothe autoinducer will be lower in cells contacted with the solution fromcells contacted with the compound than the level of detectable responsein cells contacted with the solution from cells that were not contactedwith the compound.

In some embodiments of the foregoing method, the transporter may befixed to a solid support or may be present on a cell. The transporter iscontacted with detectably labeled autoinducer in the presence or absenceof the compound and the extents of binding in the presence and absenceof the compound are compared. Alternatively, in some embodiments, theautoinducer may not be detectably labeled and the extent of autoinducerbinding is measured using an antibody that recognizes the autoinducer.

The compounds identified using any of the methods above may be furtheroptimized if desired. For example, the identified compounds may be usedas the basis for a second generation of compound libraries more closelyfocused around the original hit to determine what structural features ofthe original hit need be modified to improve, e.g., the activity,physicochemical properties, or toxicity profile of the hit. Suchapplications of this approach in an iterative fashion lead to anoptimized drug candidate.

Compounds identified using any of the methods above may be useful eitheras antimicrobial agents or as therapeutic agents. The compounds may beprovided in a form suitable for administration to a subject usingcarriers, excipients and additives or auxiliaries. Frequently usedcarriers or auxiliaries include magnesium carbonate, titanium dioxide,lactose, mannitol and other sugars, talc, milk protein, gelatin, starch,vitamins, cellulose and its derivatives, animal and vegetable oils,polyethylene glycols and solvents, such as sterile water, alcohols,glycerol and polyhydric alcohols. Intravenous vehicles include fluid andnutrient replenishers. Preservatives include antimicrobial,antioxidants, chelating agents and inert gases. Other pharmaceuticallyacceptable carriers include aqueous solutions, nontoxic excipients,including salts, preservatives, buffers and the like, as described, forinstance, in Remington's Pharmaceutical Sciences, 15th ed. Easton: MackPublishing Co., 1405-1412, 1461-1487 (1975) and The National FormularyXIV., 14th ed. Washington: American Pharmaceutical Association (1975),the contents of which are hereby incorporated by reference. The pH andexact concentration of the various components of the pharmaceuticalcomposition are adjusted according to routine skills in the art. SeeGoodman and Gilman's The Pharmacological Basis for Therapeutics (7thed.).

The pharmaceutical compositions according to the invention may beadministered locally or systemically. By “therapeutically effectivedose” is meant the quantity of a compound according to the inventionnecessary to prevent, to cure or at least partially arrest the symptomsof the disease and its complications. Amounts effective for this usewill, of course, depend on the severity of the disease and the weightand general state of the patient. Typically, dosages used in vitro mayprovide useful guidance in the amounts useful for in situ administrationof the pharmaceutical composition, and animal models may be used todetermine effective dosages for treatment of particular disorders.Various considerations are described, e.g., in Langer, Science, 249:1527, (1990); Gilman et al. (eds.) (1990), each of which is hereinincorporated by reference.

As used herein, “administering a therapeutically effective amount” isintended to include methods of giving or applying a pharmaceuticalcomposition of the invention to a subject that allow the composition toperform its intended therapeutic function. The therapeutically effectiveamounts will vary according to factors such as the degree of infectionin a subject, the age, sex, and weight of the individual. Dosage regimacan be adjusted to provide the optimum therapeutic response. Forexample, several divided doses can be administered daily or the dose canbe proportionally reduced as indicated by the exigencies of thetherapeutic situation.

The pharmaceutical composition can be administered in a convenientmanner such as by injection (subcutaneous, intravenous, etc.), oraladministration, inhalation, transdermal application, or rectaladministration. Depending on the route of administration, thepharmaceutical composition can be coated with a material to protect thepharmaceutical composition from the action of enzymes, acids and othernatural conditions that may inactivate the pharmaceutical composition.The pharmaceutical composition can also be administered parenterally orintraperitoneally. Dispersions can also be prepared in glycerol, liquidpolyethylene glycols, and mixtures thereof and in oils. Under ordinaryconditions of storage and use, these preparations may contain apreservative to prevent the growth of microorganisms.

Pharmaceutical compositions suitable for injectable use include sterileaqueous solutions (where water soluble) or dispersions and sterilepowders for the extemporaneous preparation of sterile injectablesolutions or dispersions. In all cases, the composition must be sterileand must be fluid to the extent that easy syringability exists. It mustbe stable under the conditions of manufacture and storage and must bepreserved against the contaminating action of microorganisms such asbacteria and fungi. The carrier can be a solvent or dispersion mediumcontaining, for example, water, ethanol, polyol (for example, glycerol,propylene glycol, and liquid polyetheylene glycol, and the like),suitable mixtures thereof, and vegetable oils. The proper fluidity canbe maintained, for example, by the use of a coating such as lecithin, bythe maintenance of the required particle size in the case of dispersionand by the use of surfactants. Prevention of the action ofmicroorganisms can be achieved by various antibacterial and antifungalagents, for example, parabens, chlorobutanol, phenol, ascorbic acid,thimerosal, and the like. In many cases, it will be preferable toinclude isotonic agents, for example, sugars, polyalcohols such asmannitol, sorbitol, sodium chloride in the composition. Prolongedabsorption of the injectable compositions can be brought about byincluding in the composition an agent that delays absorption, forexample, aluminum monostearate and gelatin.

Sterile injectable solutions can be prepared by incorporating thepharmaceutical composition in the required amount in an appropriatesolvent with one or a combination of ingredients enumerated above, asrequired, followed by filtered sterilization. Generally, dispersions areprepared by incorporating the pharmaceutical composition into a sterilevehicle that contains a basic dispersion medium and the required otheringredients from those enumerated above.

The pharmaceutical composition can be orally administered, for example,with an inert diluent or an assimilable edible carrier. Thepharmaceutical composition and other ingredients can also be enclosed ina hard or soft shell gelatin capsule, compressed into tablets, orincorporated directly into the individual's diet. For oral therapeuticadministration, the pharmaceutical composition can be incorporated withexcipients and used in the form of ingestible tablets, buccal tablets,troches, capsules, elixirs, suspensions, syrups, wafers, and the like.Such compositions and preparations should contain at least 1% by weightof active compound. The percentage of the compositions and preparationscan, of course, be varied and can conveniently be between about 5 toabout 80% of the weight of the unit. The amount of pharmaceuticalcomposition in such therapeutically useful compositions is such that asuitable dosage will be obtained.

The tablets, troches, pills, capsules and the like can also contain thefollowing: a binder such as gum gragacanth, acacia, corn starch orgelatin; excipients such as dicalcium phosphate; a disintegrating agentsuch as corn starch, potato starch, alginic acid and the like; alubricant such as magnesium stearate; and a sweetening agent such assucrose, lactose or saccharin or a flavoring agent such as peppermint,oil of wintergreen, or cherry flavoring. When the dosage unit form is acapsule, it can contain, in addition to materials of the above type, aliquid carrier. Various other materials can be present as coatings or tootherwise modify the physical form of the dosage unit. For instance,tablets, pills, or capsules can be coated with shellac, sugar or both. Asyrup or elixir can contain the agent, sucrose as a sweetening agent,methyl and propylparabens as preservatives, a dye and flavoring such ascherry or orange flavor. Of course, any material used in preparing anydosage unit form should be pharmaceutically pure and substantiallynontoxic in the amounts employed. In addition, the pharmaceuticalcomposition can be incorporated into sustained-release preparations andformulations.

As used herein, a “pharmaceutically acceptable carrier” is intended toinclude solvents, dispersion media, coatings, antibacterial andantifungal agents, isotonic and absorption delaying agents, and thelike. The use of such media and agents for pharmaceutically activesubstances is well known in the art. Except insofar as any conventionalmedium or agent is incompatible with the pharmaceutical composition, usethereof in the therapeutic compositions and methods of treatment iscontemplated. Supplementary active compounds can also be incorporatedinto the compositions.

It is especially advantageous to formulate parenteral compositions indosage unit form for ease of administration and uniformity of dosage.Dosage unit form as used herein refers to physically discrete unitssuited as unitary dosages for the individual to be treated; each unitcontaining a predetermined quantity of pharmaceutical composition iscalculated to produce the desired therapeutic effect in association withthe required pharmaceutical carrier. The specification for the noveldosage unit forms of the invention are dictated by and directlydependent on (a) the unique characteristics of the pharmaceuticalcomposition and the particular therapeutic effect to be achieve, and (b)the limitations inherent in the art of compounding such anpharmaceutical composition for the treatment of a pathogenic infectionin a subject.

The principal pharmaceutical composition is compounded for convenientand effective administration in effective amounts with a suitablepharmaceutically acceptable carrier in an acceptable dosage unit. In thecase of compositions containing supplementary active ingredients, thedosages are determined by reference to the usual dose and manner ofadministration of the ingredients.

As discussed briefly above, an extracellular signaling factor producedby several strains of pathogenic bacteria, including Salmonellatyphimurium and Escherichia coli, that has a role in regulating thepathogenesis or virulence of these bacteria has been identified. We havealso identified and cloned genes involved in the biosynthesis of thissignaling factor, genes that this signaling factor regulates, and genesthat encode a transporter that transports the signaling factor into thecell. The purification and/or cloning of this signaling compound and thegenes that encode proteins that catalyze its biosynthesis open a newavenue for drug design aimed at either inhibition of production of orresponse to this compound by bacteria. Drugs that interfere withsignaling by this compound will constitute a new class of antibiotics.The invention further provides methods for detecting an autoinducer andmethods for the in vitro production of autoinducer-2.

Description of the Signaling Factor

The present application provides a heterologous bioassay that hasenabled the identification of an extracellular signaling factor producedby S. typhimurium and E. coli, among other pathogenic bacteria. Thefactor is sometimes referred to herein as a “pathogenesis signaling”factor or compound, though it acts as a signal for a variety ofphysiological changes in bacteria other than pathogenesis. The factormimics the action of AI-2 (autoinducer-2) of the quorum sensingbacterium Vibrio harveyi, and it acts specifically through the V.harveyi Signaling System 2 detector, LuxQ.

The signaling factor is a small, soluble, heat labile organic compoundthat is involved in intercellular communication in all three bacteria.In E. coli and Salmonella, maximal secretion of the compound occurs inmid-exponential phase and the extracellular activity is degraded asglucose becomes depleted from the medium or by the onset of stationaryphase. Destruction of the signaling compound in stationary phaseindicates that, in constrast to other quorum sensing systems, quorumsensing in bacteria that utilize the signaling compound is critical forregulating behavior in the pre-stationary phase of growth. Proteinsynthesis is required for degradation of the activity, indicating that acomplex regulatory circuitry controls quorum sensing in these entericbacteria.

Increased signaling activity is observed if, after growing in thepresence of glucose, the bacteria are transferred to a high osmolarity(e.g., 0.4 M NaCl) or to a low pH (e.g., pH 5.0) environment. Moreover,degradation of the signal is induced by conditions of low osmolarity(e.g., 0.1 M NaCl. High osmolarity and low pH are two conditionsencountered by pathogenic enteric bacteria, such as S. typhimurium andE. coli, when they undergo the transition to a pathogenic existenceinside a host organism. Thus, quorum sensing in these bacteria appearsto play a role in regulating their virulence, by way of directing thebacteria to undergo the transition between a host-associated (i.e.,pathogenic) and a free-living existence.

Other factors that regulate the activity of the signaling compound aredescribed in greater detail in Example 2. Particularly exemplified isthe regulation of the compound in S. typhimurium.

The timing of lux induction in the bioassay and the shape of theresponse curve of V. harveyi to the S. typhimurium and E. coli signalsare indistinguishable from those of V. harveyi responding to its ownSignaling System 2 inducer, AI-2. Furthermore, each of the signalingcompounds from S. typhimurium, E. coli and V. harveyi can be partiallypurified according to the same protocol. These results indicate that thesignaling compounds from each of the aforementioned organisms are eitheridentical or very closely related.

Accordingly, AI-2 from V. harveyi is a signaling compound of theinvention, but appears to play a different role in that organism than itdoes in pathogenic enteric bacteria such as Salmonella and Escherichia.

A. Structure of the AI-2 Signaling Factor

Autoinducer-2 (AI-2) signaling factor and derivatives thereof can beused to regulate bacterial growth in a variety of applications.Autoinducer-2 compounds may have the structure:

wherein R₁, R₂, R₃ and R₄ are independently selected from hydrido, halo,alkyl, haloalkyl, cycloalkyl, cycloalkenyl, heterocyclyl, methyl, cyano,alkoxycarbonyl, amino, carboxyl, hydroxyl, formyl, nitro, fluoro,chloro, bromo, methyl, aryl, heteroaryl, aralkyl, heteroarylalkyl,alkylsulfonyl, haloalkylsulfonyl, arylsulfonyl, heteroarylsulfonyl,hydroxyalkyl, mercaptoalkyl, alkoxyalkyl, ary-loxyalkyl,heteroaryloxyalkyl, aralkyloxyalkyl, heteroarylalkyloxyalkyl,alkylthioalkyl, arylthioalkyl, heteroarylthioalkyl, aralkylthioalkyl,heteroarylalkylthioalkyl, haloalkylcarbonyl, haloalkyl(hydroxy)alkyl,alkylcarbonyl, arylcarbonyl, aralkylcarbonyl, heteroarylcarbonyl,heteroarylalkylcarbonyl, carboxyalkyl, alkoxycarbonylalkyl,alkylcarbonyloxyalkyl, aminoalkyl, alkylaminoalkyl, arylaminoalkyl,aralkylaminoalkyl, heteroarylaminoalkyl, heteroarylalkylaminoalkyl,alkoxy, and aryloxy; phenyl, cyclohexyl, cyclohexenyl, benzofuryl,benzodioxolyl, furyl, imidazolyl, thienyl, thiazolyl, pyrrolyl,oxazolyl, isoxazolyl, triazolyl, pyrimidinyl, isoquinolyl, quinolinyl,benzimidazolyl, indolyl, pyrazolyl and pyridyl, aminosulfonyl, fluoro,chloro, bromo, methylthio, methyl, ethyl, isopropyl, tertbutyl,isobutyl, pentyl, hexyl, cyano, methoxycarbonyl, ethoxycarbonyl,isopropoxycarbonyl, tertbutoxycarbonyl, propoxycarbonyl, butoxycarbonyl,isobutoxycarbonyl, pentoxycarbonyl, methylcarbonyl, fluoromethyl,difluoromethyl, trifluoromethyl, chloromethyl, dichloromethyl,trichloromethyl, pentafluoroethyl, heptafluoropropyl,difluorochloromethyl, dichlorofluoromethyl, difluoroethyl,difluoropropyl, dichloroethyl, dichloropropyl, methoxy, methylenedioxy,ethoxy, propoxy, n-butoxy, hydroxymethyl, hydroxyethyl, methoxymethyl,ethoxymethyl, trifluoromethoxy, methylamino, N,N-dimethylamino,phenylamino, ethoxycarbonylethyl, and methoxycarbonylmethyl, methyl,ethyl, fluoromethyl, difluoromethyl, trifluoromethyl, cyano,methoxycarbonyl, ethoxycarbonyl, tertbutoxycarbonyl, benzyl,phenylethyl, phenylpropyl, methylsulfonyl, phenylsulfonyl,trifluoromethylsulfonyl, hydroxymethyl, hydroxyethyl, methoxymethyl,ethoxymethyl, methylcarbonyl, ethylcarbonyl, trifluoromethylcarbonyl,trifluoro(hydroxy)ethyl, phenylcarbonyl, benzylcarbonyl,methoxycarbonylmethyl, ethoxycarbonylethyl, carboxymethyl,carboxypropyl, methylcarbonyloxymethyl, phenyloxy, phenyloxymethyl,thienyl, furyl, and pyridyl, wherein the thienyl, furyl, pyridyl,methylthio, methylsulfinyl, methyl, ethyl, isopropyl, tertbutyl,isobutyl, pentyl, hexyl, cyano, fluoromethyl, difluoromethyl,trifluoromethyl, chloromethyl, dichloromethyl, trichloromethyl,pentafluoroethyl, heptafluoropropyl, difluorochloromethyl,dichlorofluoromethyl, difluoroethyl, difluoropropyl, dichloroethyl,dichloropropyl, methoxy, methylenedioxy, ethoxy, propoxy, n-butoxy,hydroxymethyl, hydroxyethyl and trifluoromethoxy.

The chemical groups disclosed herein are known to those of skill in theart. In addition, alkyl groups refer to “lower alkyl” groups having oneto about ten carbon atoms. Most preferred are lower alkyl groups havingone to about six carbon atoms. Examples of such groups include methyl,ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tertbutyl,pentyl, isoamyl, hexyl and the like. The term “halo” means halogens suchas fluorine, chlorine, bromine or iodine. The terms “carboxy” or“carboxyl” denotes —CO2H. The term “carbonyl”, whether used alone orwith other terms, denotes —(S═O)—.

Preferably, the autoinducer-2 is 4,5-dihydroxy-2,3-pentanedione:

As used herein, an “autoinducer-2 (AI-2)” includes a compound that actsas a diffusable sensor for quorum sensing Signaling System 2. Forexample, AI-2 can regulate gene expression by increasing or decreasingexpression of genes associated with pathogenesis of a microorganism.Typically, autoinducers are produced by microorganisms, such asbacteria, during metabolism. For example, the autoinducer-2 (AI-2) ofthe invention can interact with LuxP, which is the protein encoded bythe homologue of the luxP gene of pathogenic bacteria such as V.cholerae, S. typhimurium and E. coli. In turn, the AI-2-LuxP complex caninteract with LuxQ, which is the protein product encoded by the luxQgene. The AI-2-LuxP-LuxQ interaction promotes luminescence in bacteriasuch as Vibrio spp. The AI-2-LuxP-LuxQ interaction has been linked tothe activation of biochemical pathways required for bacterialpathogenicity. Thus, bacterial gene expression can be controlled andbacterial pathogenicity can be regulated by modulating AI-2-LuxP-LuxQinteractions.

AI-2 enters the cell through the action of a transporter such as thatcomprising the LsrA, LsrB, LsrC and LsrD proteins provided herein.Accordingly, bacterial gene expression can be controlled and bacterialpathogenicity can be regulated by modulating the expression or activityof the LsrA, LsrB, LsrC and LsrD proteins or proteins homologousthereto.

Homocysteine may also be used as an autoinducer. The structure ofhomocysteine is as follows:

Homocysteine is produced by the activity of the LuxS protein onS-ribosylhomocysteine (FIG. 16). Thus, homoserine may be used as anautoinducer.

Isomers of an autoinducer-2, including both optical isomers andstructural isomers may also be used in the methods of the presentinvention.

In addition to isomers, analogs of an autoinducer-2 may be used in themethods of the present invention. As used herein, an AI-2 “analog”includes compounds that are structurally similar but not identical tothe claimed autoinducer 4,5-dihydroxy-2,3-pentanedione. Analogs of AI-2can include compounds that inhibit rather than stimulate the activity ofthe LuxP protein or compounds that block the transport of AI-2 into thecell. For example, an analog of AI-2 that can interact nonproductivelywith LuxP or that block the transport of AI-2 into the cell can beproduced. Such a compound can retain the ability to bind to LuxP or tothe AI-2 transporter (such as an AI-2 transporter comprising the LsrA,LsrB, LsrC and LsrD proteins or proteins homologous thereto), but theanalog AI-2-LuxP complex will not be able to productively interact withLuxQ or the analog AI-2-transporter complex will block the entry of AI-2into the cell, resulting in an inhibition of bacterial pathogenicity.Thus, an AI-2 analog of the invention can inhibit bacterial pathogenesisby competing with endogenous AI-2 for binding to LuxP or to the AI-2transporter. In addition, an analog of AI-2 can be constructed such thatthe analog AI-2-LuxP complex can interact nonproductively with LuxQ. Inthis case, the analog AI-2-LuxP-LuxQ complex is rendered nonfunctionalfor subsequent biochemical processes such as, for example,transcriptional activation of genes required for pathogenicity. Theinvention also includes AI-2 analogs that act synergistically to enhancethe ability of AI-2 to increase the activity of the LuxP protein.

B. Preparation of the Signaling Factor

Initial strategies for purifying the signaling compound resulted in apartially purified preparation comprising the compound with a specificsignaling activity estimated at about 0.1-1.0 mg of the partiallypurified material stimulating a 1,000-fold increase in luminescence, asmeasured in the V. harveyi bioassay. The signaling activity does notextract quantitatively into organic solvents and it does not bind toeither a cation or an anion exchange column. The compound is a small(less than 1,000 kDa), polar but uncharged organic factor. The activityis acid stable and base labile, and it is heat resistant to 80° C. butnot 100° C. These features of the signaling compound make clear that thecompound differs from any previously described autoinducer.

The signaling factor of the present invention may be purified from itsnatural sources, i.e. the bacteria that produce it. With regard topurifying AI-2 from natural sources, altering the culture medium, e.g.,by adding glucose or another sugar, by increasing the osmolarity, and/ordecreasing pH, can increase production of the signaling compound inSalmonella and other enteric bacteria, has also enabled purification ofthe signaling compound to near-homogeneity. Thus, the compound has nowbeen highly purified from culture fluids of enteric bacteria (e.g., E.coli, S. typhimurium) using the following protocol:

1. Grow a culture of the signal producing enteric bacterium overnight inLB containing 0.5% glucose or another sugar (37° C., with aeration).Inoculate fresh LB containing glucose or another sugar at 0.5% with theovernight culture, at a 1:100 dilution. Grow the diluted culture tomid-exponential phase (3.5 h, 37° C., with aeration).

2. Pellet the cells (10,000 rpm, 10 min, 4° C.). Discard the culturemedium. Resuspend the cells and wash in 1/10 th the original volume oflow osmolarity NaCl solution (0.1 M NaCl in water).

3. Pellet the cells again (10,000 rpm, 10 min, 4° C.). Discard the lowosmolarity culture fluid. Resuspend the cells in 1/10 th the originalvolume of high osmolarity NaCl solution (0.4 M NaCl in water). Incubatethe suspension at 37° C. for 2 h with aeration. During this time,increased production and secretion of the signaling compound occurs.

4. Pellet the cells (10,000 rpm, 10 min, 4° C.). Collect the supernatantcontaining the secreted signaling compound, filter the supernatantthrough a 0.2 M bacterial filter to remove any remaining cells.

5. Evaporate the aqueous filtrate using a rotary evaporator at 30° C.Extract the dried filtrate in 1/10 th the original volume ofchloroform:methanol (70:30).

6. Evaporate the organic extract using a rotary evaporator at roomtemperature. Redissolve the dried extract in methanol at 1/100 th of theoriginal volume.

7. Subject the partially purified signal to High Performance LiquidChromatography (HPLC), using a preparative reverse phase C18 column.Elute the compound with a linear gradient of 0-100% acetonitrile inwater at 5 ml per minute. Collect 30 fractions, 5 ml each.

8. Assay the HPLC fractions in the V. harveyi BB170 AI-2 assay, and poolthe active fractions.

The product from the C18 column contains the signaling compound and asmall number of other organic compounds. This highly purifiedpreparation of the signaling compound has activity 50-100 times greaterthan that of the partially purified material described above (thepreparation of which did not include the high osmoticum step or thefinal HPLC step), i.e., 1-10 μg material stimulates a 1,000-foldincrease in luminescence in the V. harveyi bioassay.

Subsequent strategies for purifying the AI-2 signaling compound have ledto the identification of a novel in vitro system for producing AI-2.Thus, in addition to providing a cloned, overexpressed and purified S.typhimurium LuxS protein, the application also provides a method forproducing AI-2 in vitro. The application provides a mechanism forgenerating large quantities of pure AI-2 useful for mass spectral andNMR analysis, and for screening compounds that regulate the activity ofAI-2. Moreover, the present application provides a method fordetermining the in vivo biosynthetic pathway for AI-2 synthesis. The invitro method for AI-2 production is described below in Example 5 andFIG. 16. The method provides a novel means for efficiently producingautoinducers for further study. The method also provides a means forproducing substantial quantities of AI-2 for use in commercialapplications. Such applications include, but are not limited to, addingAI-2 of the invention to a growth medium to increase bacterial growth.Such a method is particularly useful in the in the production ofantibiotics from cultured bacteria. The addition of AI-2 can increasethe antibiotic production of such organisms by promoting cell growth.Preferably, the signaling factor AI-2 is produced by the in vitro methodset forth in Example 5 of the disclosure.

C. Uses of the Signaling Factor

The isolated and purified signaling compounds of the present inventionare used as targets for the design of compounds that regulate theactivity of AI-2, such as compounds that modulate the transport of AI-2into the cell. As used herein, “regulate” includes increasing ordecreasing the activity of AI-2. As used herein, the “activity” of AI-2encompasses any aspect of the compound's ability to act as a signalingfactor in bacterial quorum sensing. A “compound” can be any agent orcomposition that effects the activity of AI-2 For example, a compound ofthe invention can be a nucleic acid, a protein or small molecule. Thus,the invention provides a means for identifying a new class ofantibiotics that inhibit the activity of the AI-2 or otherwise block thesignaling pathway in which the compound participates. Such inhibitorsmay be identified by large-scale screening of a variety of testcompounds, using the V. harveyi or Salmonella typhimurium bioassay inthe presence of the purified signaling compound. A reduction insignaling activity in the presence of a test compound would beindicative of the ability of that compound to inhibit the activity ofthe signaling compound or to block some other part of the pathogenesissignaling pathway such as the transport of AI-2 into the cell.

Further, the invention provides a basis for the rational design ofspecific inhibitors or nonfunctional analogs of AI-2. Suchstructure-specific inhibitors or analogs may be tested in the V. harveyior Salmonella typhimurium bioassay for their ability to inhibit thesignaling compound, the ability to inhibit the transport of thesignaling compound into the cell, or the ability to block thepathogenesis signaling pathway.

The invention also encompasses methods for identifying naturallyproduced compounds that inhibit the activity of a signaling compoundsuch as autoinducer-2 or the transport of the signaling compound intothe cell. For example, a defensive strategy employed by eucaryoticorganisms to avoid bacterial colonization is to specifically target andinhibit quorum sensing controlled functions. Such a mechanism has beenidentified in D. pulchra. Recent studies indicate that halogenatedfuranones produced by D. pulchra inhibit quorum sensing by competing forthe homoserine-lactone (HSL) autoinducer-binding site in LuxR. Thus, byproviding a novel auto-inducer and the cellular components that interactwith the autoinducer, the present application also provides a method toscreen naturally produced compounds for their effect on quorum sensingsystem-2. For example, naturally produced compounds can be screened fortheir effect on the autoinducer-2-LuxP interaction or their effect onthe transport of AI-2 into the cell. Alternatively, such compounds canbe screened for their effect on autoinducer-2-LuxP-LuxQ interactions.

It will be appreciated by persons skilled in the art that, now thattargets for the signaling compound have been identified in E. coli,inhibition of the E. coli target can also be used to screen potentialsignaling compound inhibitors or analogs. The inventors have prepared aler-lacZ reporter fusion construct to be used in testing for reductionof expression of the Type III secretion gene in E. coli O157:H7(pathogenic strain) directly. Alternatively, E. coli strains having analtered expression level of a transporter that transports AI-2 into thecell may be generated using methods such as those described herein andused to screen signaling compound inhibitors or analogs. Furthermore, asimilar locus exists in S. typhimurium.

Thus, the application provides a method for selecting inhibitors orsynergists of the autoinducer-2,4,5-dihydroxy-2,3-pentanedione. As usedherein, an “inhibitor” of AI-2 is intended to include compounds thatinterfere with the ability of the autoinducer to act as a signal forluminescence or pathogenesis. Inhibitors include compounds that degradeor bind to AI-2. The method comprises contacting the autoinducer with asuspected inhibitor or synergist, measuring the ability of the treatedautoinducer to stimulate the activity of a selected gene thendetermining whether the suspected inhibitor or synergist represses orenhances the activity of the autoinducer. Actual inhibitors andsynergists of the autoinducer are then selected. For example, asuspected inhibitor can be mixed with 4,5-dihydroxy-2,3-pentanedione andthe mixture then combined with a reporter strain of V. harveyi disclosedherein. The amount of luminescence in the presence of the suspectedinhibitor can be compared with a control mixture that does not includethe inhibitor. A decrease in luminescence indicates AI-2 inhibition. Inthis manner, compounds that regulate bacterial pathogenesis can berapidly screened.

One aspect of the invention is a method for identifying a compound thatmodulates (i.e. increases or decreases) the response to an autoinducerthat is not an acyl-homoserine lactone. Such compounds may be usefuleither as antimicrobial agents or as therapeutic agents. In someembodiments, the autoinducer may be AI-2 from Vibrio harveyi, apentadione, or 4,5-dihydroxy-2,3-pentadione, or an autoinducer that isnot an acylhomoserine lactone and that is able to interact with theVibrio harveyi luxQ protein, thereby inducing expression of a Vibrioharveyi operon comprising the luxCDABE genes. A cell that produces adetectable signal in response to the autoinducer is obtained and theresponse of the cell to the autoinducer is measured in the presence andabsence of a test compound. The responses of the cells to theautoinducer in the presence and absence of the test compound arecompared to determine whether the compound modulates the response to theautoinducer.

The cell may be from any desired species that produces a detectablesignal in response to the autoinducer or a cell that has been engineeredto produce a detectable signal in response to the autoinducer. In someembodiments, the cell is a Vibrio harveyi cell. In other embodiments,the cell may be a Salmonella typhimurium, E. coli, Haemophilusinfluenza, Helicobacter pylori, Bacillus subtilis, Borrelia burdorferior Vibrio cholerae cell.

The cell may produce any detectable signal in response to theautoinducer. For example, in some embodiments, the cell producesbioluminescence in response to the autoinducer. Thus, in someembodiments, the cell is a Vibrio harveyi cell that producesbioluminescence in response to the autoinducer via induction of theluxCDABE operon.

Alternatively, in some embodiments, the detectable signal may beinduction of mRNA transcription or protein expression in response to theautoinducer. Induction of mRNA transcription may be measured with any ofa variety of techniques familiar to those skilled in the art, includingNorthern analysis or detection of the transcript through use of nucleicacid amplification techniques such as PCR. Induction of proteinexpression may also be measured with any of a variety of techniquesfamiliar to those skilled in the art including gel electrophoresis,Western blotting, or enzymatic activity assays. For example, in someembodiments, the cell may be genetically engineered to express a markerprotein such as -galactosidase, chloramphenicol acetyltransferase,β-glucuronidase, luciferase or green fluorescent protein in response tothe autoinducer. Thus, in some embodiments, a nucleic acid encoding themarker protein may be operably linked to the luxCDABE promoter andintroduced into the cell such that expression of the marker protein isinduced by the autoinducer. Alternatively, in other embodiments, anautoinducer responsive promoter other than the luxCDABE promoter may beoperably linked to a nucleic acid encoding the marker protein. The theautoinducer responsive promoter may be from the same species as the cellto be used in the method or, alternatively, the the autoinducerresponsive promoter may be from a heterologous organism.

The response of the cell to the autoinducer is measured in the presenceand absence of a test compound. The test compound may benaturally-occuring, such as a compound from a natural products library,or may be of synthetic origin, such as a compound generated through useof combinatorial chemistry.

The response of the cell to the autoinducer in the presence and absenceof the test compound is compared. In some embodiments, the test compoundalters the response to the autoinducer at least two fold, at least 10fold, at least 20 fold, at least 50 fold, at least 100 fold, at least1000 fold, or even more than 1000 fold.

In some embodiments, the cell that produces a detectable signal inresponse to the autoinducer has a genetic alteration that inhibitsproduction of the autoinducer. In some embodiments, the geneticalteration is introduced into the cell through use of such geneticengineering techniques as site directed mutagenesis, insertionalmutagenesis, or chemical mutagenesis followed by appropriate selection.Alternatively, cells containing the genetic alteration may be isolatedor selected from a natural population.

In some embodiments, the genetic alteration that inhibits production ofthe autoinducer is in the Vibrio harveyi luxS gene, a gene havinghomology to the Vibrio harveyi luxS gene, or a gene encoding apolypeptide having homology to the Vibrio harveyi luxS polypeptide. Forexample, the genetic alteration may be in a gene having a sequence withat least 50%, at least 60%, or at least 80% sequence homology to theVibrio harveyi luxS gene. In other embodiments the genetic alteration isin a gene encoding a polypeptide having at least 57% or at least 85%homology to the Vibrio harveyi luxS polypeptide. In still furtherembodiments, the genetic alteration is in a gene encoding a polypeptidehaving at least 32%, at least 45%, at least 74% or at least 80% sequenceidentity to the Vibrio harveyi luxS polypeptide.

In some embodiments, the cells have a first genetic alteration thatinhibits production of an autoinducer that is not an acyl-homoserinelactone and a second genetic alteration that inhibits detection orresponse to another autoinducer that is an acyl-homoserine lactone. Forexample, in some embodiments, the cell is a Vibrio harveyi cell, thefirst genetic aleration is in the luxS gene and the second geneticalteration is in the luxN gene. Thus, in some embodiments, the cell maybe a Vibrio harveyi MM32 cell as described herein. However, the firstand second genetic alterations may be in any gene that provides thephenotypeds discussed above, including the genes discussed above, andthe cell may be from any suitable species, including the speciesspecifically enumerated herein.

In another aspect, the invention also provides methods of selectinginhibitory and synergistic analogs of AI-2. The method comprises mixinga known amount of the autoinducer with a known amount of the suspectedinhibitory or synergistic analog, measuring the ability of the treatedautoinducer to stimulate the activity of a selected gene thendetermining whether the suspected inhibitory or synergistic analogrepresses or enchances the activity of the autoinducer. Actualinhibitory or synergistic analogs of the autoinducer are then selected.

Autoinducer-2 can be purified from the native source through use ofconventional purification techniques, derived synthetically by chemicalmeans, or preferably, produced by the in vitro method of the inventiondescribed below. As used herein, “purified from a native source”includes an autoinducer-2 of the above formula that has been manufactureby an organism. “Purified from the native source” includes isolating theautoinducer from the culture medium or cytoplasm of bacteria such as S.typhimurium through use of conventional purification techniques. As usedherein, “synthesized by chemical means” includes autoinducers of theclaimed formula that have been artificially produced outside of anorganism. The invention includes an autoinducer of the inventionmanufactured by a person skilled in the art from chemical precursorsthrough use of standard chemical synthesis techniques.

The application further provides methods of inhibiting the infectivityof a pathogenic organism as well as therapeutic compositions containingan AI-2 analog or AI-2 inhibitor of the invention. The methods compriseadministering to a subject a therapeutically effective amount of anpharmaceutical composition that inhibits the activity of AI-2, thetransport of AI-2 into the cell, or the repression of genes that encodepolypeptides involved in the transport of AI-2 into the cell. As usedherein, “inhibiting infectivity” includes methods of affecting theability of a pathogenic organism to initially infect or further infect asubject that would benefit from such treatment. A pharmaceuticalcomposition of the invention can include, but is not restricted to, anagent that prevents the transcriptional activation of extracellularvirulence factors such as exotoxin A and elastolytic proteases or anagent that inhibits tht transport of AI-2 into the cell. As used herein,an “agent” includes compounds that inhibit the ability of the LuxPprotein and LuxQ protein to activate transcription of extracellularvirulence factors and compounds that inhibit the transport of AI-2 intothe cell. Agents include inhibitors that interact directly with AI-2such that AI-2 is prevented from acting as a sensor for quorum sensingSignaling System-2. Preferably, the agent interacts with4,5-dihydroxy-2,3-pentanedione. Agents further include analogs of AI-2that can compete with 4,5-dihydroxy-2,3-pentanedione for binding toLuxP, LuxQ, or the transporter that transports AI-2 into the cell.

The application further provides pharmaceutical compositions forpreventing or treating pathogen-associated diseases by targeting factorsinvolved in the Signaling System type-2 pathway. For example, LsrA,LsrB, LsrC, LsrD, LsrE, LsrF, LsrG, LsrR, LuxP or LuxQ, or homologuesthereof, provide a common target for the development of a vaccine.Antibodies raised to LsrA, LsrB, LsrC, LsrD, LsrE, LsrF, LsrG, LsrR,LuxP or LuxQ or homologues thereof, can inhibit the activation ofbacterial pathways associated with virulence. Thus, LsrA, LsrB, LsrC,LsrD, LsrE, LsrF, LsrG, LsrR, LuxP or LuxQ provide common antigenicdeterminants that can be used to immunize a subject against multiplepathogen-associated disease states. For example, the autoinducerSignaling System type-2 is believe to exist in a broad range ofbacterial species including bacterial pathogens. As discussed above, theautoinducer-2 signaling factor is believed to be involved ininterspecies as well as intraspecies communication. In order for thequorum sensing Signaling System type-2 to be effective for interspeciescommunication, it is likely to be highly conserved among variousbacterial species. Thus, challenging a subject with the LsrA, LsrB,LsrC, LsrD, LsrE, LsrF, LsrG, LsrR, LuxP or LuxQ polypeptide, or anantigenic fragment thereof, isolated from a particular organism mayconfer protective immunity to other disease states associated with adifferent organism. For example, a vaccine developed to the LuxP proteinisolated from V. cholerae may be capable of cross-reacting with a LuxPhomologue expressed by a different organism. Thus, it is envisioned thatmethods of the present invention can be used to treatpathogen-associated disease states.

Generally, the terms “treating”, “treatment”, and the like are usedherein to mean obtaining a desired pharmacologic and/or physiologiceffect. The effect may be prophylactic in terms of completely orpartially preventing a spirochete infection or disease or sign orsymptom thereof, and/or may be therapeutic in terms of a partial orcomplete cure for an infection or disease and/or adverse effectattributable to the infection or disease. “Treating” as used hereincovers any treatment of (e.g., complete or partial), or prevention of,an infection or disease in a mammal, particularly a human, and includes:

a) preventing the disease from occurring in a subject that may bepredisposed to the disease, but has not yet been diagnosed as having it;

b) inhibiting the infection or disease, i.e., arresting its development;or

c) relieving or ameliorating the infection or disease, i.e., causeregression of the infection or disease.

Thus, the invention includes various pharmaceutical compositions usefulfor ameliorating symptoms attributable to a bacterial infection or,alternatively, for inducing a protective immune response to prevent suchan infection. For example, a pharmaceutical composition according to theinvention can be prepared to include an antibody against, for example,LsrA, LsrB, LsrC, LsrD, LsrE, LsrF, LsrG, LsrR, LuxP or LuxQ, a peptideor peptide derivative of LsrA, LsrB, LsrC, LsrD, LsrE, LsrF, LsrG, LsrR,LuxP or LuxQ mimetic, or a LsrA, LsrB, LsrC, LsrD, LsrE, LsrF, LsrG,LsrR, LuxP or LuxQ-binding agent. The pharmaceutical agent may beformulated as described above.

In addition to generating antibodies that bind to antigenic epitopes ofproteins of the invention, it is further envisioned that the method ofthe invention can be used to induce cellular responses, particularlycytotoxic T-lymphocytes (CTLs), to antigenic epitopes of, for exampleLsrA, LsrB, LsrC, LsrD, LsrE, LsrF, LsrG, LsrR, LuxP or LuxQ. Typically,unmodified soluble proteins fail to prime major histocompatibilitycomplex (MHC) class I-restricted CTL responses whereas particulateproteins are extremely immunogenic and have been shown to prime CTLresponses in vivo. CTL epitopes and helper epitopes have been identifiedin proteins from many infectious pathogens. Further, these epitopes canbe produced concurrently such that multiple epitopes can be delivered ina form that can prime MHC class I restricted CTL responses. An exampleof a system that can produce recombinant protein particles carrying oneor more epitopes entails the use of the p1 protein of theretrotransposon Ty1 of Saccharomyces cerevisiae (Adams, et al., Nature,329:68, 1987). Sequences encoding CTL epitopes can, for example, befused to the C-terminus of p1 and the resulting Ty virus-like particles(Ty-VLPs) may be able to generate a CTL response. Thus, conservedregions of pathogenic antigens, such as those that are involved in, orresult from, the activation of Signaling System type-2, can beidentified and incorporated together in a particle that enables the hostimmune system to mount an effective immune response against multiplespirochetal organisms. Further, the method of the invention can be usedto generate particles with multiple epitopes to a single protein, suchas LuxP, or multiple epitopes from various proteins.

The method of the invention also includes slow release antigen deliverysystems such as microencapsulation of antigens into liposomes. Suchsystems have been used as an approach to enhance the immunogenicity ofproteins without the use of traditional adjuvants. Liposomes in theblood stream are generally taken up by the liver and spleen, and areeasily phagocytosed by macrophages. Liposomes also allow coentrapment ofimmunomodulatory compounds along with the antigens, so that suchcompounds may be delivered to the site of antigen encounter, allowingmodulation of the immune system towards protective responses.

In another embodiment, the invention provides a method for identifying acompound that binds to a protein of the invention, such as LsrA, LsrB,LsrC, LsrD, LsrE, LsrF, LsrG, LsrR, LuxP or LuxQ or to a complexcomprising one or more of the foregoing proteins. The method includesincubating components comprising the compound and LsrA, LsrB, LsrC,LsrD, LsrE, LsrF, LsrG, LsrR, LuxP or LuxQ or a complex comprising oneor more of the foregoing proteins under conditions sufficient to allowthe components to interact and measuring the binding of the compound toLsrA, LsrB, LsrC, LsrD, LsrE, LsrF, LsrG, LsrR, LuxP or LuxQ or thecomplex comprising one or more of the foregoing proteins. Compounds thatbind to LsrA, LsrB, LsrC, LsrD, LsrE, LsrF, LsrG, LsrR, LuxP or LuxQinclude peptides, peptidomimetics, polypeptides, chemical compounds andbiologic agents as described above.

Incubating includes conditions that allow contact between the testcompound and LsrA, LsrB, LsrC, LsrD, LsrE, LsrF, LsrG, LsrR, LuxP orLuxQ or a complex comprising one or more of the foregoing proteins.Contacting includes in solution and in solid phase. The testligand(s)/compound may optionally be a combinatorial library forscreening a plurality of compounds. Compounds identified in the methodof the invention can be further evaluated, detected, cloned, sequenced,and the like, either in solution or after binding to a solid support, byany method usually applied to the detection of a specific DNA sequencesuch as PCR, oligomer restriction (Saiki, et al., B--io/-Technology,3:1008-1012, 1985), allele-specific oligonucleotide (ASO) probe analysis(Conner, et al., Proc. Natl. Acad. Sci. USA, 80:278, 1983),oligonucleotide ligation assays (OLAs) (Landegren, et al., Science,241:1077, 1988), and the like. Molecular techniques for DNA analysishave been reviewed (Landegren, et al., Science, 242:229-237, 1988). Alsoincluded in the screening method of the invention are combinatorialchemistry methods for identifying chemical compounds that bind to LsrA,LsrB, LsrC, LsrD, LsrE, LsrF, LsrG, LsrR, LuxP or LuxQ. See, forexample, Plunkett and Ellman, “Combinatorial Chemistry and New Drugs”,Scientific American, April, p. 69, (1997).

The application further provides a method for promoting the productionof a bacterial product, such as, for example, an antibiotic, bycontacting a culture of bacteria with an AI-2 of the invention at aconcentration effective to stimulate or promote cellular metabolism,growth or recovery. For example, it is known that antibiotic-producingbacteria only produce an antibiotic at or near the peak of log phasegrowth. By contacting a culture medium containing suchantibiotic-producing bacteria with AI-2 of the invention, production ofan antibiotic can be induced at an earlier phase of growth. Thus, AI-2of the invention provides a method for increasing the amount ofantibiotic produced by a culture. “Culture medium”, as used herein, isintended to include a substance on which or in which cells grow. Theautoinducer can be included in commercially available cell culture mediaincluding broths, agar, and gelatin.

The invention further provides a method for identifying factors thatdegrade or inhibit the synthesis of autoinducer-2. For example, it isknown that autoinducer-1 concentration peaks in mid- to late log phaseof a bacterial cell culture. In contrast, autoinducer-2 concentrationincreases earlier in log phase of bacterial cell culture growth and ispresent in lower amounts in late log phase and stationary phase. Thisdata indicates that a mechanism exists for the degradation ofautoinducer-2 at a specific point in bacterial growth. By providingisolated and purified autoinducer-2, the application allows for theidentification of the mechanism whereby autoinducer-2 levels arecontrolled. For example, partially purified bacterial extracts can beassayed against isolated autoinducer-2 to identify those fractions thatdegrade autoinducer-2. Fractions that degrade autoinducer-2 can befurther fractionated by techniques known to those skilled in the artuntil those cellular components involved in autoinducer degradation areisolated.

The present invention also provides a method of regulating theexpression of a gene. The method comprises inserting a gene intobacteria chosen for enhancement of gene expression by an agent capableof stimulating the activity of the LuxQ protein and incubating thebacteria with an agent capable of stimulating the activity of the LuxPprotein. Thus, the signaling compound of the invention can also be usedin screens for other targets that it regulates. Cloned promoter-fusionlibraries can be prepared from any species of bacteria and theselibraries can be used to identify genes that are induced or repressed bythe signaling factor, simply by screening for differences in reporteractivity in Petri or microtiter plates containing the signaling compoundcompared to plates that do not contain the compound.

In addition, quorum sensing is a major regulator of biofilm control andquorum sensing blockers can therefore be used to prevent and/or inhibitbiofilm formation. Also, quorum sensing blockers are effective inremoving, or substantially decreasing the amount of, biofilms that havealready formed on a surface. Thus, by providing the structure ofautoinducer-2 (AI-2), the present invention provides a new approach toidentifying compounds that inhibit bacterial infections by regulatingbiofilm formation.

It is known that quorum sensing blockers can reduce protease productionby 50% in some strains of bacteria but the discovery that certaincompounds can substantially eliminate protease production imparts clearclinical advantages. Furthermore, the unexpected finding that biofilmformation can be inhibited or prevented by quorum sensing blockers leadsto the reasonable conclusion that other quorum sensing blockers that areknown to exhibit quorum sensing blocking in other systems, such asprotease production, will also be effective against biofilm formation.

The compounds of the invention are advantageously used to treat and/orprevent infections, such as those caused by V. angufflarum or Aeromonasspp. Examples of this type of infection are vibriosis and furunculosisdisease in fish. Inhibition of biofilm formation by the bacteria,optionally together with a reduction or elimination of extracellularprotease production, renders the bacteria substantially nonpathogenic.The compounds of the invention may be formulated by conventional methodsfor use in the treatment and/or prevention of bacterial infection. Forexample, the compounds may be used as solid or liquid preparations (suchas tablets, suspensions or solutions for oral administration or sterileinjectable compositions), optionally together with pharmaceuticallyacceptable diluents, carriers or other additives.

For the treatment of vibriosis or furunculosis disease in fish, thecompounds or compositions containing them may be applied directly to thefish or they may be added to the fish's food or water.

In another embodiment, the invention provides a method of removing abiofilm from a surface that comprises treating the surface with acompound of the invention. The surface is preferably the inside of anaqueous liquid distribution system, such as a drinking waterdistribution system or a supply line connected to a dental air-watersystem. The removal of biofilms from this type of surface can beparticularly difficult to achieve. The compound is preferably applied tothe surface as a solution of the compound either alone or together withother materials such as conventional detergents or surfactants.

A further embodiment of the invention is an antibacterial compositioncomprising a compound of the invention together with a bacteriocidalagent. In the antibacterial compositions, the compound of the inventionhelps to remove the biofilm whilst the bacteriocidal agent kills thebacteria. The antibacterial composition is preferably in the form of asolution or suspension for spraying and/or wiping on a surface.

In yet another aspect, the invention provides an article coated and/orimpregnated with a compound of the invention in order to inhibit and/orprevent biofilm formation thereon. The article is preferably of plasticsmaterial with the compound of the invention distributed throughout thematerial.

Description of Nucleic Acids Encoding Proteins Involved in SignalingFactor Biosynthesis

The genes responsible for production of the signaling compound of theinvention in V. harveyi, S. typhimurium and E. coli have been cloned andcharacterized. These genes encode a novel family of proteins responsiblefor autoinducer production. We have designated the members of thisfamily of autoinducer production genes as luxS, specificallyluxS_(E.c.), luxS_(S.t.), and luxS_(V.h.) for E. coli, S. typhimuriumand V. harveyi respectively.

Mutagenesis of luxS in V. harveyi, S. typhimurium and E. coli eliminatesproduction of the signaling compound in all three species of bacteria.S. typhimurium could be complemented to full production of the compoundby the introduction of either the E. coli O157:H7 luxS_(E.c.) gene orthe V. harveyi BB120 luxS_(V.h.) gene. These results indicate that boththe E. coli and V. harveyi LuxS proteins can function with S.typhimurium cellular components to produce the signaling compound. E.coli DH5 was only partially complemented to production of the signalingcompound by the introduction of either the E. coli O157:H7 luxS_(E.c.)or the V. harveyi BB120 luxS_(V.h.) gene. Because in trans expression ofluxS genes in E. coli DH5 did not completely restore signaling compoundproduction, other biochemical or physiological factors may contribute tosignal production.

The regulation of signaling compound production differs betweenpathogenic and nonpathogenic strains. For example E. coli O157:H7strains produce AI-2 at 30° and 37° C. with or without glucose while E.coli K-12 strains do not produce the compound in the absence of apreferred carbon source. And, all of the E. coli O157 strains testedproduce greater signaling activity than do non-pathogenic E. colistrains. Likewise, pathogenic S. typhimurium 14028 producessignificantly more signaling activity than does S. typhimurium LT2.

Sequence analysis shows that the LuxS proteins are highly homologous,and complementation data suggest that the proteins can function acrossspecies. These results indicate that the enzymatic activity carried outby the LuxS proteins and any other cellular machinery that contributesto synthesis of the signaling compound are conserved. We did notidentify any sequence motif in the LuxS proteins that indicates aparticular function. Therefore, the LuxS proteins most likely catalyzeone specific enzymatic step in biosynthesis of the signaling compound.The remainder of the steps involved in signaling compound biosynthesiscould result from normal intermediary metabolic processes. The luxSgenes identified here bear no homology to other genes known to beinvolved in production of acyl-homoserine lactone autoinducers(luxI-like (Fuqua et al., J. Bacteriol. 176, 269-275, 1994),luxLM-ainS-like (Bassler et al, 1993, supra; Gilson et al, J. Bacteriol.177, 6946-6951, 1995), further indicating that the signaling compoundsdescribed herein are novel.

Database analysis of finished and unfinished bacterial genomes revealsthat many other species of bacteria possess a gene homologous to luxSfrom V. harveyi, S. typhimurium and E. coli. The species of bacteriaidentified and the percent homology/identity (H/I) to the LuxS proteinof V. harveyi are as follows: Haemophilus influenzae (88/72),Helicobacter pylori (62/40), Bacillus subtilis (58/38), Borreliaburgfdorferi (52/32), Neisseria meningitidis (89/80), Neisseriagonorrhoeae (89/80), Yersinia pestis (85/77), Campylobacter jejuni(85/74), Vibrio cholerae (95/90), Deinococcus radiodurans (65/45),Mycobacterium tuberculosis (59/41), Enterococcus faecalis (60/44),Streptococcus pneumoniae (57/36) and Streptococcus pyogenes (57/36). Asreported earlier (Bassler et al., 1997, supra), a few of these specieswere tested for production of the signaling compound. We showed that V.cholerae and Y. enterocolitica but not B. subtilis produced signalingactivity. We believe that B. subtilis does produce the compound but theenvironmental conditions that induce its synthesis have not yet beendetermined. Furthermore, we believe that all of the species identifiedin the database analysis produce an AI-2-like compound.

The sequences of the luxS genes from V. harveyi, E. coli and S.typhimurium are set forth at the end of the specification as SEQ ID NO:1, SEQ ID NO:2 and SEQ ID NOS:3 and 4, respectively (the sequences readin the 5′ to 3′ direction). These genes are sometimes referred to hereinas “LuxS_(V.h.)”, “LuxS_(E.c.)” and “LuxS_(S.t.)”, respectively. Thesequences deduced from SEQ ID NOS: 1-4 are set forth at the end of thespecification (and in FIG. 13) as SEQ ID NO:10, SEQ ID NO:11 and SEQ IDNO:12, respectively. It is believed that SEQ ID NOS:1 and 2 constitutefull-length clones, whereas SEQ ID NO:3 and SEQ ID NO:4 do not.

The LuxS genes from V. harveyi, E. coli and S. typhimurium are describedin greater detail in Example 3. Although those particular luxS genes andtheir encoded proteins are exemplified herein, this inventionencompasses luxS genes and their encoded enzymes from any bacterialspecies, having the sequence, structural and functional properties ofthe luxS-encoded proteins described herein. As mentioned in Example 3,homologous nucleic acid sequences have been identified in a variety ofbacterial species, but identity of those sequences as luxS genesheretofore had not been appreciated. LuxS nucleotide and deduced aminoacid sequences from other bacterial species are set forth at the end ofthe specification as SEQ ID NOS: 5-9 and 13-17, respectively, andinclude sequences from the following species: Haemophilus influenzae,Helicobacter pylori, Bacillus subtilis, Borrelia burgdorferi and Vibriocholerae.

In addition to LuxS homologs from species other than V. harveyi, E. colior S. typhimurium, variants and natural mutants of SEQ ID NOS:1-9 arelikely to exist within different species or strains of Vibrio,Escherichia and Salmonella (indeed, E. coli strain DH5 possesses anon-functional mutant form of the gene). Because such variants areexpected to possess certain differences in nucleotide and amino acidsequence, this invention provides an isolated LuxS nucleic acid andencoded protein having at least about 50-60% (preferably 60-80%, mostpreferably over 80%) sequence homology in the coding region with thesequences set forth as SEQ ID NOS:1-9, respectively (and, preferably,specifically comprising the coding regions of SEQ ID NOS:1-9), and thesequence of SEQ ID NOS:10-17. Because of the natural sequence variationlikely to exist among these proteins and nucleic acids encoding them,one skilled in the art would expect to find up to about 40-50% sequencevariation, while still maintaining the unique properties of theluxS-encoded proteins of the present invention. Such an expectation isdue in part to the degeneracy of the genetic code, as well as to theknown evolutionary success of conservative amino acid sequencevariations, which do not appreciably alter the nature of the protein.Accordingly, such variants are considered substantially the same as oneanother and are included within the scope of the present invention.

For purposes of this invention, the term “substantially the same” refersto nucleic acid or amino acid sequences having sequence variation thatdo not materially affect the nature of the protein (i.e. the structuralcharacteristics and/or biological activity of the protein). Withparticular reference to nucleic acid sequences, the term “substantiallythe same” is intended to refer to the coding region and to conservedsequences governing expression, and refers primarily to degeneratecodons encoding the same amino acid, or alternate codons encodingconservative substitute amino acids in the encoded polypeptide. Withreference to amino acid sequences, the term “substantially the same”refers generally to conservative substitutions and/or variations inregions of the polypeptide not involved in determination of structure orfunction. The terms “percent identity” and “percent similarity” are alsoused herein in comparisons among amino acid sequences. These terms areintended to be defined as they are in the UWGCG sequence analysisprogram (Devereaux et al., Nucl. Acids Res. 12: 387-397, 1984),available from the University of Wisconsin, and the default parametersused by that program are the parameters intended to be used herein tocompare sequence identity and similarity.

A. Preparation of Nucleic acids, Encoded Proteins, and ImmunologicallySpecific Antibodies

1. Nucleic Acids

LuxS nucleic acids of the invention may be prepared by two generalmethods: (1) They may be synthesized from appropriate nucleotidetriphosphates, or (2) they may be isolated from biological sources. Bothmethods utilize protocols well known in the art.

The availability of sequence information, such as the DNAs having SEQ IDNOS:1-9, enables preparation of an isolated nucleic acid of theinvention by oligonucleotide synthesis. Synthetic oligonucleotides maybe prepared by the phosphoramadite method employed in the AppliedBiosystems 38A DNA Synthesizer or similar devices. The resultantconstruct may be purified according to methods known in the art, such ashigh performance liquid chromatography (HPLC). Long, double-strandedpolynucleotides, such as a DNA of the present invention, must besynthesized in stages, due to the size limitations inherent in currentoligonucleotide synthetic methods. Such long double-stranded nucleicacids may be synthesized as several smaller segments of appropriatecomplementarity. Complementary segments thus produced may be annealedsuch that each segment possesses appropriate cohesive termini forattachment of an adjacent segment. Adjacent segments may be ligated byannealing cohesive termini in the presence of DNA ligase to construct anentire 1.8 kb double-stranded nucleic acid. A synthetic DNA soconstructed may then be cloned and amplified in an appropriate vector.

LuxS nucleic acids also may be isolated from appropriate biologicalsources using methods known in the art. In a preferred embodiment, agenomic clone is isolated from a cosmid expression library of an S.typhimurium or E. coli genome. In another embodiment, a genomic clone isisolated from a cosmid library of another bacterial genome.

In accordance with the present invention, nucleic acids having theappropriate level sequence homology with the protein coding region ofany of SEQ ID NOS:1-9 may be identified by using hybridization andwashing conditions of appropriate stringency. For example,hybridizations may be performed, according to the method of Sambrook etal., using a hybridization solution comprising: 5×SSC, 5× Denhardt'sreagent, 1.0% SDS, 100 g/ml denatured, fragmented salmon sperm DNA,0.05% sodium pyrophosphate and up to 50% formamide. Hybridization iscarried out at 37-42NC for at least six hours. Following hybridization,filters are washed as follows: (1) 5 minutes at room temperature in2×SSC and 1% SDS; (2) 15 minutes at room temperature in 2×SSC and 0.1%SDS; (3) 30 minutes-1 hour at 37° C. in 1×SSC and 1% SDS; (4) 2 hours at42-65Nin 1×SSC and 1% SDS, changing the solution every 30 minutes.

One common formula for calculating the stringency conditions required toachieve hybridization between nucleic acids of a specified sequencehomology (Sambrook et al., 1989):T _(m)=81.5C+16.6Log [Na⁺]+0.41(% G+C)−0.63 (% formamide)−600/#bp induplex

As an illustration of the above formula, using [Na⁺]=[0.368] and 50%formamide, with GC content of 42% and an average probe size of 200bases, the T_(m) is 57C. The T_(m) of a DNA duplex decreases by 1-1.5°C. with every 1% decrease in homology. Thus, targets with greater thanabout 75% sequence identity would be observed using a hybridizationtemperature of 42° C.

Another way to isolate the luxS nucleic acids is to search the publiclyavailable databases for the luxS sequence in the bacterial genome ofinterest, design PCR primers from the sequence and amplify the genedirectly from the chromosome. The PCR product can then be cloned.Alternatively, if the complete sequence of a specific bacterial genomeis not available, the sequences set forth in the present invention, orany other luxS sequence, may be used to design degenerateoligonucleotides for PCR amplification and cloning of luxS from thechromosome.

Nucleic acids of the present invention may be maintained as DNA in anyconvenient cloning vector. In a preferred embodiment, clones aremaintained in plasmid cloning/expression vector, such as pBluescript(Stratagene, La Jolla, Calif.), which is propagated in a suitable E.coli host cell.

LuxS nucleic acids of the invention include DNA, RNA, and fragmentsthereof that may be single- or double-stranded. Thus, this inventionprovides oligonucleotides (sense or antisense strands of DNA or RNA)having sequences capable of hybridizing with at least one sequence of anucleic acid of the present invention, such as selected segments of theDNA having SEQ ID NOS:1, 2 or 3. Such oligonucleotides are useful asprobes for detecting LuxS genes or transcripts.

LsrA, LsrB, LsrC, LsrD, LsrE, LsrF, LsrG, or LsrR nucleic acids andnucleic acids homologous thereto may also be prepared and used asdescribed above.

2. Proteins and Antibodies

A full-length LuxS gene product of the present invention may be preparedin a variety of ways, according to known methods. The protein may bepurified from appropriate sources, e.g., cultured bacteria such as S.typhimurium, E. coli or V. harveyi.

The availability of full-length LuxS nucleic acids enables production ofthe encoded protein using in vitro expression methods known in the art.According to a preferred embodiment, the enzyme may be produced byexpression in a suitable expression system. For example, part or all ofa DNA, such as the DNA having SEQ ID NO:1 or 2, may be inserted into aplasmid vector adapted for expression in a bacterial cell, such as E.coli, or a eucaryotic cell, such as Saccharomyces cerevisiae or otheryeast. Such vectors comprise the regulatory elements necessary forexpression of the DNA in the host cell, positioned in such a manner asto permit expression of the DNA in the host cell. Such regulatoryelements required for expression include promoter sequences,transcription initiation sequences and, optionally, enhancer sequences.

The protein produced by LuxS gene expression in a recombinantprocaryotic or eucyarotic system may be purified according to methodsknown in the art. In a preferred embodiment, a commercially availableexpression/secretion system can be used, whereby the recombinant proteinis expressed and thereafter secreted from the host cell, to be easilypurified from the surrounding medium. If expression/secretion vectorsare not used, an alternative approach involves purifying the recombinantprotein by affinity separation, such as by immunological interactionwith antibodies that bind specifically to the recombinant protein. Suchmethods are commonly used by skilled practitioners.

The protein encoded by the LuxS gene of the invention, prepared by oneof the aforementioned methods, may be analyzed according to standardprocedures. For example, the protein may be subjected to amino acidsequence analysis, according to known methods. The stability andbiological activity of the enzyme may be determined according tostandard methods, such as by the ability of the protein to catalyzeproduction of the signaling compound under different conditions.

The present invention also provides antibodies capable ofimmunospecifically binding to the LuxS-encoded protein of the invention.Polyclonal antibodies may be prepared according to standard methods. Ina preferred embodiment, monoclonal antibodies are prepared, which reactimmunospecifically with various epitopes of the protein. Monoclonalantibodies may be prepared according to general methods of Köhler andMilstein, following standard protocols. Polyclonal or monoclonalantibodies that immunospecifically interact with the LuxS-encodedproteins can be utilized for identifying and purifying such proteins.For example, antibodies may be utilized for affinity separation ofproteins with which they immunospecifically interact. Antibodies mayalso be used to immunoprecipitate proteins from a sample containing amixture of proteins and other biological molecules.

LsrA, LsrB, LsrC, LsrD, LsrE, LsrF, LsrG, or LsrR proteins, proteinshomologous thereto or antibodies that recognize the foregoing proteinsmay also be prepared as described above.

B. Uses of Nucleic acids, Encoded Protein and Immunologically SpecificAntibodies

LuxS nucleic acids may be used for a variety of purposes in accordancewith the present invention. DNA, RNA, or fragments thereof may be usedas probes to detect the presence of and/or expression of LuxS genes.Methods in which LuxS nucleic acids may be utilized as probes for suchassays include, but are not limited to: (1) in situ hybridization; (2)Southern hybridization (3) northern hybridization; and (4) assortedamplification reactions such as polymerase chain reactions (PCR).

The LuxS nucleic acids of the invention may also be utilized as probesto identify related genes from other bacteria. As is well known in theart, hybridization stringencies may be adjusted to allow hybridizationof nucleic acid probes with complementary sequences of varying degreesof homology.

As described above, LuxS nucleic acids are also used to advantage toproduce large quantities of substantially pure encoded protein, orselected portions thereof. It should be noted in this regard that thecloned genes inserted into expression vectors can be used to make largequantities of the signaling compound itself, from any selected bacterialspecies, in a recombinant host such as E. coli DH5. Specific luxS genesare cloned, a large quantity of the encoded protein produced, therebyproducing a large quantity of the specific signaling compound. This willbe particularly useful determining differences in the structures ofsignaling compounds from different species, if such differences arefound to exist. Alternatively, a large quantity of signaling compoundfrom the species of interest could be made using the cloned gene in anexpression vector, and thereafter used in library screens for potentialtargets in petri plate assays, as described above.

Purified LuxS gene products, or fragments thereof, may be used toproduce polyclonal or monoclonal antibodies that also may serve assensitive detection reagents for the presence and accumulation of thoseproteins in cultured cells. Recombinant techniques enable expression offusion proteins containing part or all of a selected LuxS-encodedprotein. The full length protein or fragments of the protein may be usedto advantage to generate an array of monoclonal or polyclonal antibodiesspecific for various epitopes of the protein, thereby providing evengreater sensitivity for detection of the protein in cells or tissue.Other uses of the LuxS proteins include overproduction to make aquantity of the LuxS proteins sufficient for crystallization. Solvingthe crystal structure of the LuxS proteins would enable the exactdetermination of the LuxS active site for catalysis of production of thesignaling compound. The LuxS crystal structure can therefore be used forcomputer modeling that would greatly facilitate design of signalingcompound analogs, LuxS inhibitors, and rational drug design in general.

Polyclonal or monoclonal antibodies immunologically specific for aLuxS-encoded protein may be used in a variety of assays designed todetect and quantitate the protein. Such assays include, but are notlimited to: (1) flow cytometric analysis; (2) immunochemicallocalization of a LuxS protein in cells or tissues; and (3) immunoblotanalysis (e.g., dot blot, Western blot) of extracts from various cellsand tissues. Additionally, as described above, antibodies can be usedfor purification of the proteins (e.g., affinity column purification,immunoprecipitation).

LsrA, LsrB, LsrC, LsrD, LsrE, LsrF, LsrG, or LsrR nucleic acids, nucleicacids homologous thereto, encoded proteins, proteins homologous theretoor antibodies that recognize the foregoing proteins may also be used asdescribed above.

Vibrio Harveyi Screening Strain

In another aspect, the application provides a novel strain of VibrioHarveyi having a genotype that is luxN⁻, luxS⁻. In some embodiments ofthe present invention, such a strain may be used to generate a strainthat overexpresses or underexpresses a transporter that transports AI-2into the cell relative to a wild type strain. The Gram-negativebacterium Vibrio harveyi contains two parallel quorum sensing circuitsthat synthesize and detect two different autoinducers (FIG. 13). Circuit1 synthesizes AI-1 a HSL autoinducer similar in structure toautoinducers synthesized by the Luxl/R pathway found in otherGram-negative bacteria. Circuit 2 synthesizes AI-2, the structure ofwhich has not been determined. Synthesis of AI-1 and AI-2 is dependenton LuxLM and LuxS respectively. Following the buildup of a criticalexternal concentration of the autoinducers, signaling occurs via aseries of a phosphorylation/dephosphorylation reactions. The AI-1 andAI-2 detectors, LuxN and LuxQ respectively, contain both a sensor kinasedomain with a conserved histidine (H1) and an attached responseregulator domain with a conserved aspartate (D1). Signals from bothsensors are channeled to the shared integrator protein LuxU, which isphosphorylated on a histidine residue (H2). Subsequently, the signal istransduced to a conserved aspartate residue (D2) on the responseregulator protein LuxO. LuxO-phosphate controls the expression of theluciferase structural operon luxCDABE that results in the emission oflight. The presence of either AI-1 or AI-2 is sufficient to turn onlight production in wild-type V. harvyi (strain BB120). For this reason,we have V. harvyi strains containing separate mutations in Lux genes L,M, S or Q that are defective in their ability to synthesize or detectAI-1 or AI-2, respectively. AI-2 is detectable using strain BB170 thatis sensor 1⁻, sensor 2⁺ (LuxN⁻, LuxQ⁺). This strain was used to detectAI-2 in diverse bacteria. The light emission response of wild type,LuxN− and LuxQ− phenotypes to increasing cell density is shown in FIG.15.

BB170 is a sensitive reporter for AI-2, however, the BB170 strain is notoptimal for use as a reporter for inhibitors of the quorum pathway in amicrotiter based assay. The desired strain is defective in its abilityto detect AI-1 (sensor 1⁻) and defective in its ability to synthesizeAI-2. Thus, the invention provides a strain of V. harveyi that isgenotypically luxN⁻ and luxS⁻. The new strain, designated MM32, isuseful for identifying inhibitors of the quorum sensing pathway. Forexample, since the new strain is sensor 1⁻, its growth or ability toluminesce will not be affected by those organisms producing AI-1.Further, since MM32 is defective for production of AI-2, the addition ofexogenous AI-2, or analogs thereof, allows for the rapid identificationof modulators (activators or inhibitors) of AI-2.

In addition, the materials described above are ideally suited for thepreparation of a kit. Such a kit may comprise a carrier means beingcompartmentalized to receive in close confinement one or more containermeans such as vials, tubes, and the like, each of the container meanscomprising one of the separate elements to be used in the method.

The container means may comprise a strain of bacteria capable ofdetecting the presence of an autoinducer. Preferably, the bacterialstrain will be capable of providing an easily detectable signal in thepresence of autoinducer-2. More preferably, the desired strain isdefective in its ability to detect AI-1 (sensor 1⁻) and defective in itsability to synthesize AI-2. Thus, the kit may provide a strain of V.harveyi that is genotypically luxN⁻ and luxS⁻ designated MM32. Thebacterial strain is useful for identifying autoinducer-2 as well asmodulators (activators and inhibitors) of autoinducer-2 and the quorumsensing pathway.

Methods for Detecting a Bacterial Biomarker

Many bacteria presently known to utilize the autoinducer-l signalingfactor associate with higher organisms, i.e., plants and animals, atsome point during their lifecycles. For example, Pseudomonas aeruginosais an opportunistic pathogen in humans with cystic fibrosis.P.aeruginosa regulates various virulence determinants with AI. Otherexamples of AI producing bacteria include Erwinia carotovora,Pseudomonas aureofaciens, Yersinia enterocolitica, Vibrio harveyi, andAgrobacterium tumefaciens. E. carotovora infects certain plants andcreates enzymes that degrade the plant's cell walls, resulting in whatis called “soft rot disease.” Yersinia enterocolitica is a bacteriumthat causes gastrointestinal disease in humans and has been reported toproduce an autoinducer. P.aureofaciens associates with the roots ofplants and produces antibiotics that block fungus growth in the roots.The antibiotic synthesis is under autoinducer control. The presentinvention provides novel autoinducer-2 and methods of usingautoinducer-2. In contrast to autoinducer-1, autoinducer-2 is believedto be an intra-species as well as inter-species signaling factor.Autoinducer-2 is further believed to regulate the expression ofpathogenic and virulence factors not regulated by autoinducer-1. Thus,the present invention provides a method to identify and regulate theexpression of bacterial biomarkers in, for example, pathogenic bacteria.Methods of the invention can be used to regulate the activity ofbacterial pathogens that are present in both plants and animals.

The application further provides a method for detecting anautoinducer-associated bacterial biomarker by contacting at least onebacterial cell with an autoinducer under conditions and for such time asto promote induction of a bacterial biomarker. In some embodiments, thecell may have an increased expression level of a transporter thattransports the autoinducer into the cell relative to a wild type cell.As used herein, an “autoinducer-associated bacterial biomarker” is anybacterial cell component that is regulated, modified, enhanced,inhibited or induced in response to an autoinducer. A biomarker can beany bacterial cell component that is identifiable by known microscopial,histological or molecular biological techniques. Such biomarkers can beused, for example, to distinguish pathogenic from nonpathogenicbacteria. Such a biomarker can be, for example, present on a cellsurface, and it can be a protein, a nucleic acid, a phosphorylationevent or any molecular or morphological characteristic of a bacterialcell that is modified as a result of the bacterium being contacted withan autoinducer. Preferably, the autoinducer is autoinducer-2. The methodof the invention is particularly useful for identifying a biomarker thatindicates bacterial pathogenicity. As previously noted, autoinducers areextracellular signalling factors used by a variety of bacteria toregulate cellular functions in response to various environmentalstimuli, including high population density. It is believed thatpathogenic bacteria express a biomarker, such as an antigenicdeterminant, as a result of increased autoinducer concentration in thesurrounding environment. Thus, the present invention provides a methodfor identifying a biomarker by contacting a bacterium with autoinducer-2and assaying for the presence of the biomarker.

The method of the invention contemplates the use of a probe to identifya biomarker present in a bacterial cell. As used herein, a “probe” canbe a nucleic acid, protein, small molecule or antibody useful fordetecting a bacterial biomarker present in a sample. The probe can beused in a screening assay to identify a biomarker present in a sampleafter the sample has been contacted with, for example, an autoinducer.For example, a bacterial biomarker produced by a bacterium followingcontact with an autoinducer can can be identified by contacting a samplecontaining the bacterium with a probe that binds to the biomarker. Suchassays can be used to detect, prognose, diagnose, or monitor variousconditions, diseases, and disorders, or monitor the treatment thereof. Aprobe can be detectably labeled such that the probe is detectable whenbound to its target marker. Such means for detectably labeling a probeinclude a biotin-binding protein, such as avidin or streptavidin, boundto a reporter, such as an enzymatic, fluorescent, or radionuclide label.Other reporter means and labels are well known in the art.

In addition, the method of the invention can be used to analyzedifferential gene expression in a bacterial cell following contact withan autoinducer. In some embodiments, the cell may have an increasedlevel of expression of a transporter that transports the autoinducerinto the cell. For example, where the expression of genes in differentcells, normally a cell of interest and a control, is compared and anydiscrepancies in expression are identified. In such assays, the presenceof discrepancies indicates a difference in the classes of genesexpressed in the cells being compared. Methods that can be used to carryout the foregoing are commonly known in the art.

The present invention provides a method for identifying a biomarker thatcan be a protein. For example, a bacterial protein expressed in responseto an autoinducer can be detected using the appropriate antibody. Insome embodiments, the bacterial protein may be expressed in a cellhaving an increased expression level of a transporter that transports anautoinducer into the cell relative to a wild type cell. The expressedprotein can be, for example, an antigenic determinant indicative of apathogenic bacterium. Antibodies used in the method of the invention aresuited for use, for example, in immunoassays for the detection of such adeterminant. The term “antibody” as used herein is meant to includeintact polyclonal or monoclonal antibodies, as well as fragmentsthereof, such as Fab and F(ab′)₂,. For example, monoclonal antibodiesare made from antigen containing fragments of a protein by methods wellknown to those skilled in the art (Kohler, et al., Nature, 256:495,1975).

In addition, the monoclonal antibodies in these immunoassays can bedetectably labeled in various ways. For example, radioisotopes may bebound to an immunoglobulin either directly or indirectly by using anintermediate functional group. Intermediate functional groups that oftenare used to bind radioisotopes that exist as metallic ions toimmunoglobulins are the bifunctional chelating agents such asdiethylenetriamine-pentacetic acid (DTPA) and ethylenediaminetetraaceticacid (EDTA) and similar compounds. Typical examples of metallic ionsthat can be bound to monoclonal antibodies are ¹¹¹In, ⁹⁷Ru, ⁶⁷Ga, ⁶⁸Ga,⁷²As, ⁸⁹Zr, and ²⁰¹Tl.

A probe useful in the method of the invention can also be a nucleic acidprobe. For example, nucleic acid hybridization techniques are well knownin the art and can be used to identify an RNA or DNA biomarker presentin a sample containing a bacterium contacted with an autoinducer.Screening procedures that rely on nucleic acid hybridization make itpossible to identify a biomarker from any sample, provided theappropriate probe is available. For example, oligonucleotide probes,which can correspond to a part of the sequence encoding a targetprotein, can be synthesized chemically. The DNA sequence encoding theprotein can be deduced from the genetic code, however, the degeneracy ofthe code must be taken into account. For such screening, hybridizationis preferably performed under in vitro or in in vivo conditions known tothose skilled in the art.

In addition, the materials described above are ideally suited for thepreparation of a kit. Such a kit may comprise a carrier means beingcompartmentalized to receive in close confinement one or more containermeans such as vials, tubes, and the like, each of the container meanscomprising one of the separate elements to be used in the method. A kitof the invention may contain a first container means comprising isolatedautoinducer-2. The isolated autoinducer-2 can be used to regulate theexpression of a biomarker in a target bacterium. For example,autoinducer-2 can be used to induce expression of a particular biomarkerthat can then be identified by a probe. Thus, the kit may contain asecond container means comprising a probe that can be detectablylabeled. The kit may also have a third container comprising areporter-means, such as a biotin-binding protein, such as avidin orstreptavidin, bound to a reporter, such as an enzymatic, fluorescent, orradionuclide label. Other reporter means and labels are well known inthe art. For example, the kit of the invention may provide reagentsnecessary to perform nucleic acid hybridization analysis as describedherein or reagents necessary to detect antibody binding to a target.

AI-2 regulated genes were identified using the following strategy basedon the identification of luxS regulated target genes in S. typhimurium.MudJ transposon mutagenesis was employed to generate isogenic lacZtranscriptional fusions in wild type and luxS null strains of S.typhimurium (Hughes and Roth, 1988). Eleven thousand insertion mutantswere made and subsequently screened for differential expression of thelacZ reporter gene. The MudJ insertions from candidate luxS regulatedfusion strains were backcrossed by P22 transduction into S. typhimurium14028 (wild type) and S. typhimurium SS007 (luxS::T-POP) to verify thatthe differences observed in lacZ expression were a consequence of thepresence or absence of a functional luxS gene on the S. typhimuriumchromosome. Eight lacZ fusions that appeared to produce higher levels ofβ-galactosidase in the strain carrying the wild type luxS gene than inthe luxS null strain were identified.

The insertion sites of the eight luxS regulated MudJ fusions weredetermined by arbitrary PCR amplification of the MudJ-chromosome fusionjunctions, followed by BLAST database analysis (Caetano-Anolles, 1993;Altschul et al., 1990). One MudJ insertion was located in the metE gene.MetE is involved in the biosynthesis of methionine, that is a precursorof SAM (Weissbach and Brot, 1991). Specifically, MetE catalyzes thefinal step in methionine biosynthesis in the absence of vitamin B12.Transcription of metE is induced when the substrate homocysteine isavailable and when the intracellular concentration of methionine is low(Urbanowski and Stauffer, 1989). We reason that metE is not a truetarget of AI-2 regulation, but instead metE transcription is induced inthe wild type luxS strain relative to the luxS null strain becausehomocysteine is produced during the generation of AI-2 in the LuxS⁺strain. Consistent with this hypothesis, we found that addition ofexogenous AI-2 to the metE-lacZ insertion mutant did not affect thetranscription of the metE-lacZ fusion (not shown). We did not study themetE-lacZ fusion strain further.

The seven remaining MudJ insertions all resided in a single operon in S.typhimurium (FIG. 17, SEQ ID NO: 44). This operon is of unknown functionbut is predicted to encode an ABC transporter complex with strikingsimilarity to the ribose transport operon (Rbs) of E. coli and S.typhimurium. We have named this operon the lsr operon forluxS-regulated. FIG. 17 shows the lsr operon of S. typhimurium and thesites of the luxS regulated MudJ insertions identified in our geneticscreen.

The rbs operon of E. coli and S. typhimurium is shown in FIG. 17B. Thefunctions encoded by the rbs operon are responsible for thehigh-affinity transport and phosphorylation of ribose (FIG. 17C) (lidaet al., 1984). The rbs operon has been most extensively studied in E.coli, although the rbs operon of S. typhimurium has the same arrangementand is predicted to encode proteins with identical functions. In the rbsoperon of E. coli, the first gene, rbsD, encodes a protein with no knownfunction. RbsA, RbsB and RbsC comprise the transport apparatus (Bell etal., 1986). RbsB is the periplasmic binding protein that recognizesribose and interacts with RbsC. RbsC is the homodimeric channel-formingprotein (Park et al., 1999). RbsA is the membrane-associated ATPase thatsupplies energy to drive the transport of the sugar into the cell(Buckel et al., 1986). RbsK is a cytoplasmic kinase that phosphorylatesribose upon entry into the cell (Hope et al., 1986). Finally, RbsR isthe regulatory protein that functions at the rbs promoter to represstranscription of the operon in the absence of ribose (Mauzy andHermodson, 1992).

In the lsr operon, the first gene, lsrA, encodes a protein homologous tothe RbsA ATPase. The lsrC and lsrD genes are homologous to one anotherand to rbsC and are predicted to encode the components of aheterodimeric membrane channel. lsrB encodes a predicted sugar bindingprotein homologous to RbsB. In the lsr operon, three additional genesare located downstream of the putative ABC transporter. We have namedthese genes lsrF, lsrg and lsrE, respectively. The lsrF and lsrG genesencode proteins of unknown function, and lsrE encodes a protein withhomology to the E. coli ribulose phosphate epimerase (rpe) (Sprenger,1995). The completed genome sequence of E. coli shows that it alsopossesses this operon (Blattner et al., 1997). In the E. coli genome,the operon has been designated the b1513 operon. The b1513 operon has anarrangement identical to the S. typhimurium lsr operon except that theE. coli b1513 operon does not contain a gene homologous to lsrE. We havenot tested whether the b1513 operon is controlled by luxS in E. coli.

Analysis of the luxS regulated fusions in the lsr operon. We obtainedluxS regulated MudJ insertions in lsrA, lsrC, lsrB, lsrF and lsrE (FIG.17). The β-galactosidase activity produced by each of these lacZ fusionswas measured in wild type luxS and luxS null S. typhimurium strains(FIG. 18). Note that although we obtained three insertions in the lsrFgene, results for only one of these fusions appear in FIG. 18 becauseall three fusions have the same activity. The white bars show theβ-galactosidase activity in the luxS null strain, and the black barsshow the corresponding level of β-galactosidase activity for each fusionwhen wild type luxS is present. The figure shows that the lsrA, lsrC andlsrF fusions are induced 12- to 16-fold when wild type luxS is present.

The lsrB-lacZ and lsrE-lacZ fusions show lower activity than the fusionswe obtained in the other three genes in this operon. In the case oflsrE, as this is the gene most distal to the promoter, the low activitymay be explained by weak transcription. However, weak transcriptioncannot be the cause of the low activity observed for the lsrB-lacZfusion because we observe high activity from the downstream lsrF-lacZfusion. One explanation for the low activity in the lsrB-lacZ fusion isthat a functional LsrB protein is required for the transcription of thelsr operon. To test this hypothesis, we constructed an inframe deletionof lsrB and demonstrated that it did not affect transcription of any ofthe other lsr-lacZ fusions (not shown). Furthermore, although theabsolute β-galactosidase units are low for the lsrB-lacZ fusion, thefold induction of this fusion in the wild type luxS strain over the luxSnull strain is about the same as that of all the other fusions weobtained in lsr genes. Based on these results, we conclude that thisparticular fusion joint is uncommonly polar, and results in lower thanexpected transcription of lacZ, which would account for its reducedβ-galactosidase activity.

To verify that the induction of transcription of the lsr operon is dueto luxS, we complemented the fusion strains with the luxS gene in trans.FIG. 18 shows these data. In a luxS null S. typhimurium background,introduction of the parent vector without luxS had no effect on theβ-galactosidase expression of the lsr fusions (gray bars). However,introduction of the cloned luxS gene into each of the lsr-lacZ fusionstrains restored β-galactosidase activity to nearly the level observedfor the fusions in the wild type luxS background (striped bars).

AI-2 regulates the transcription of the lsr operon. The above resultsshow that the lsr operon is induced in the presence of a functional luxSgene. In earlier work, we have shown that the LuxS enzyme catalyzes thefinal step in the biosynthesis of AI-2 (Schauder et al., 2001). Weinterpret our above results to mean that regulation of the lsr operon byluxS is mediated by the presence of AI-2. We further predict that AI-2should exert its regulatory effect on the lsr operon by signalling fromthe outside of the cell. However, the strategy we used to identify thelsr operon relies on internal production of AI-2 in S. typhimurium. Toprove that AI-2 is sufficient for lsr regulation, and also to prove thatexternal AI-2 is capable of mediating this effect, we tested whetherexogenously supplied AI-2 could induce the lsr-lacZ fusions in S.typhimurium strains containing a null mutation in luxS.

We have previously reported that AI-2 is synthesized fromS-adenosylhomocysteine (SAH) in two steps by the action of the Pfs andLuxS enzymes (Schauder et al., 2001). Specifically, SAM is used as aubiquitous intracellular methyl donor. SAH is formed when the methylgroup of SAM is transferred to its various substrates. Pfs cleavesadenine from SAH to form SRH, and LuxS cleaves SRH to form homocysteineand AI-2. In that report we developed a procedure for the in vitroproduction of S. typhimurium AI-2 from SAH using purified Pfs and LuxSproteins (Schauder et al., 2001). We can estimate the AI-2 concentrationin our in vitro preparations indirectly by measuring the concentrationof homocysteine that is produced along with AI-2 by LuxS. Using AI-2prepared by this method, we tested the effect of the exogenous additionof AI-2 on the regulation of the S. typhimurium lsr operon.

Various S. typhimurium lsr::MudJ fusion strains were grown to lateexponential phase in LB medium supplemented with AI-2 prepared by our invitro method at an approximate concentration of 70 μM. This is roughlytwice the concentration of AI-2 that we estimate to be present in S.typhimurium cell-free supernatants (not shown). As a control, weperformed the same experiment with material from in vitro reactionscarried out with SAH and Pfs enzyme in the absence of the LuxS enzyme.This reaction produces adenine and SRH. Homocysteine was added to thiscontrol mixture following the reaction to compensate for thehomocysteine that would be produced by LuxS. Therefore, the onlycomponent absent from the control reaction was AI-2. The β-galactosidasemeasurements in FIG. 19 show that, in the presence of the −AI-2 controlreaction, low expression of the lsr-lacZ fusions occurs in the absenceof luxS (white bars), and similar to those shown in FIG. 18, the fusionsare induced to varying degrees in the presence of wild type luxS (blackbars). In strains lacking luxS, addition of 70 μM exogenous AI-2 inducesthe expression of the lsr-lacZ fusions to levels above that when wildtype luxS is present on the chromosome (gray bars). This experimentshows that exogenous AI-2 is sufficient for induction of the lsr operonin S. typhimurium.

We also supplied exogenous AI-2 to the S. typhimurium lsr-lacZ fusionstrains that were wild type for luxS on the chromosome (striped bars).FIG. 19 shows that increasing the level of AI-2 above the endogenouslevel produced by chromosomal luxS results in an additional stimulationof the expression of the lsr-lacZ fusions. This result indicates that,under the conditions that we are performing our experiments, the lsroperon is not fully induced by the endogenously produced AI-2.

Identification of LsrR: a protein responsible for mediating AI-2regulation of transcription of the lsr operon. The above results showthat AI-2 induces the expression of the lsr operon. However, because noDNA binding protein is encoded in the lsr operon, we did not understandhow the presence of AI-2 could modulate the transcription of the lsroperon. We hypothesized that a DNA binding protein must exist in S.typhimurium that functions to couple the presence of the AI-2 signal toexpression of the lsr operon. To identify this regulatory factor, weperformed a genetic selection for mutants in which the Lac⁻ phenotype ofa luxS null, lsr-lacZ fusion strain was suppressed. Our reasoning was asfollows: all of the luxS null strains containing lacZ fusions in the lsroperon do not grow on lactose minimal plates. However, the presence of afunctional luxS gene on the chromosome induces the expression of thelacZ gene in these fusions to a sufficient level to restore growth onlactose minimal plates. Therefore, selection for growth of a luxS null,lsr-lacZ S. typhimurium strain on lactose minimal plates enabled us toisolate S. typhimurium colonies that had acquired spontaneous suppressormutations that allowed increased expression of the lsr-lacZ fusion inthe absence of luxS (i.e., in the absence of AI-2). We performed thisexperiment with the representative lsrC-lacZ strain. Eight spontaneousLac⁺ colonies were isolated by this technique and studied further. Wealso used a transposon mutagenesis strategy to identify the putativeregulatory factor. Mutagenesis with the transposon T-POP was performedon the luxS null, lsrC-lacZ fusion strain. 12,000 insertions were made,and two transposon insertion mutants were identified that restoredgrowth to the luxS null, lsrC-lacZ strain on lactose minimal medium.

Linkage analysis showed that the T-POP insertions and the spontaneoussuppressor mutations could be co-transduced with high frequency (76%co-transduction) with the lsrC::MudJ insertion. Database analysis of theS. typhimurium genome revealed that a gene encoding a predicted DNAbinding protein of unknown function is located immediately upstream ofthe lsr operon but is transcribed divergently (FIG. 17). This protein ishomologous to SorC, a DNA binding protein that functions as both anactivator and a repressor of transcription of genes involved in sorbosemetabolism in Klebsiella pneumoniae (Wehmeier and Lengeler, 1994). Wepredicted that the transposon and spontaneous suppressor mutations couldbe located in this gene. Indeed, we were able to PCR amplify thechromosome-T-POP fusion junction from both T-POP suppressor strainsusing primers specific to T-POP and the regions flanking this putativeregulatory gene. In addition, we PCR amplified and sequenced thisregulatory gene from the chromosome of the eight spontaneous suppressorstrains. In every case, this gene was found to contain either a pointmutation or a deletion. We have named this gene lsrR, for regulator ofthe lsr operon. Because inactivation of the lsrR gene results inhigh-level expression of the lsr operon in a luxS null background, theseresults strongly suggest that the wild type function of LsrR is torepress the expression of the lsr operon in the absence of AI-2.

Deletion of lsrR results in unregulated transcription of the lsr operon.To verify the role of LsrR in AI-2 regulation of lsr operontranscription, we constructed an inframe deletion of lsrR in S.typhimurium and assayed the expression of the lsr-lacZ fusions in thepresence and absence of lsrR. The results are shown in FIG. 20 for therepresentative lsrC-lacZ reporter fusion. The first pair of bars showsthat, as in FIG. 18, when wild type lsrR is present, lsrC-lacZexpression is repressed in a luxS null strain and derepressed 23-foldwhen luxS is present and the AI-2 signal is synthesized (white and blackbar, respectively). In contrast, the second pair of bars shows thatdeletion of lsrR results in high-level expression (over 100-foldderepression) of the lsrC-lacZ reporter whether or not luxS is present.This result demonstrates that the lsr operon cannot be regulated by AI-2in the absence of LsrR. We cloned the wild type lsrR gene and expressedit in trans under an exogenous promoter to show that LsrR couldcomplement the ΔlsrR defect. The third and fourth pairs of bars in FIG.20 show that in trans expression of lsrR in both wild type lsrR andAlsrR S. typhimurium strains causes repression of the lsrC-lacZ reporterfusion. Specifically, complete repression of lsrC-lacZ transcriptionoccurs in the luxS null strains (white bars), and nearly completerepression of lsrC-lacZ transcription occurs in the wild type luxSstrains (black bars). These results show that introduction of lsrRcomplements the ΔlsrR defect. However, when lsrR is overexpressed in awild type luxS background, the AI-2 produced is apparently insufficientto compensate for the increased LsrR protein produced by the vector.This imbalance results in incomplete inactivation of LsrR by AI-2, solsr operon repression occurs. We performed control experiments to showthat expression of the parent vector without the cloned lsrR gene had noeffect on lsrC-lacZ activity in any of these strains (not shown).

Analysis of the LsrR suppressor mutations. The sequence of the LsrRprotein is shown in FIG. 21 as well as the spontaneous mutations weidentified in the suppressor selection. The β-galactosidase activitiesof the spontaneous lsrR mutations were measured and compared to that ofwild type lsrR and the lsrR deletion. Again, the lsrC-lacZ fusion isused as the representative reporter for the lsr operon. Results areshown in FIG. 22. The two left-most bars show the control experiments inwhich lsrC-lacZ expression is measured in the luxS null and wild typeluxS strains. Both of these strains contain wild type lsrR. As shownabove, expression of lsrC-lacZ is derepressed in the wild type luxSstrain compared to the luxS null strain (in this case, 9-fold). Theremaining bars in FIG. 22 represent the activities of various lsrRmutants in a luxS null background. Specifically, mutations A22T, A120Tand G208R result in an increase in expression of the lsrC-lacZ fusion toabout the same level as that when wild type luxS is present (6- to10-fold). Compared to the ΔlsrR strain, we observe an intermediate levelof lsrC-lacZ expression in an lsrR mutant with a deletion encompassingthe N-terminus of the protein and part of the lsr promoter (Δ5′) andfrom mutations resulting in the alterations L145Q and L134P(approximately 80-fold derepression). Maximal derepression of lsrC-lacZoccurs in the L39P and Y25H mutants. We know this is maximalderepression of the operon because the activities of these two missensemutants equal that caused by the null lsrR::T-POP and ΔlsrR mutations(approximately 250-fold derepression). The L39P point mutation islocated in the predicted helix turn helix DNA binding domain, apparentlyeliminating the repressor function of the protein. Apparently, the Y25residue is critical for function, or this particular alteration simplycannot be tolerated. Note that although we obtained two T-POP insertionsin lsrR, the activity for only one of the insertions is shown. Bothinsertions gave identical results in this experiment.

The Lsr ABC transporter has a role in elimination of extracellular AI-2.The lsr operon apparently encodes an ABC transporter resembling theribose transporter. As AI-2 is a ribose derivative, we hypothesize thatAI-2 could be the ligand for the Lsr transporter complex. Therefore, onepossible function of the Lsr operon is to transport the AI-2 synthesizedby LuxS in the cytoplasm out of the S. typhimurium cell. Thispossibility seems unlikely because the lsr operon encodes a transporterwith homology to binding protein-dependent ABC transporters thatfunction to import compounds into the cytoplasm (Nikaido and Hall,1998). Moreover, mutants with insertions in the lsr operon are notdeficient in AI-2 production, indicating that the Lsr transporter is notrequired for export of the AI-2 signal into the medium (not shown).

We have previously reported that, in S. typhimurium, extracellular AI-2activity accumulates to maximal levels in late exponential phase, andsubsequently the AI-2 activity disappears from the medium (Surette andBassler, 1998; 1999). Additionally, we have shown that AI-2 in cell-freeculture fluids remains active for long periods of time, indicating thatthe disappearance of the activity from the extracellular environment isnot due to instability of AI-2 (Surette and Bassler, 1999). Furthermore,we have shown that elimination of AI-2 from the medium requires proteinsynthesis (Surette and Bassler, 1999). Therefore, an alternativepossibility for the function of the Lsr complex is to importextracellular AI-2 into the cytoplasm of S. typhimurium. We performed anexperiment to investigate this possibility.

Cultures of S. typhimurium luxS null strains containing a wild type lsroperon or containing mutations inactivating lsr genes were grown tomid-exponential phase in LB at 37° C. AI-2 prepared by our in vitromethod was added to the cultures, and the cultures were incubated withthe AI-2 for an hour. Subsequently, the cells were removed from theculture fluid by centrifugation, and the resulting cell-free culturefluids were assayed for AI-2 activity using the V. harveyi AI-2bioassay. This assay involves measuring the increase in light productionof a V. harveyi quorum sensing reporter strain that inducesbioluminescence exclusively in response to the presence of AI-2. In thepresent experiment, the bioassay allowed us to determine the level ofAI-2 activity remaining in the culture fluids of the different S.typhimurium mutants. Since all the S. typhimurium strains we used inthis experiment contained null mutations in luxS, the only AI-2 thatcould be present in the cell-free culture fluids came from that that weadded exogenously.

FIG. 23 shows the results of this experiment. The control experimentshows that, as expected, no AI-2 activity is present in culture fluidsprepared from the S. typhimurium luxS null strain used as the parent forthese studies. The bar labeled “Input” shows that AI-2 sufficient toinduce the V. harveyi bioluminescence reporter 1000-fold was added tothe remainder of the cultures. The input activity was measured by addingAI-2 to the parent S. typhimurium culture and immediately chilling theculture on ice, followed by centrifugation of the cells and isolation ofthe cell-free culture fluid. The figure shows that 1 h incubation of thewild type lsr strain with the input AI-2 results in disappearance of 92%of the AI-2 activity from the culture fluid, as activity sufficient toinduce the bioassay strain only 80-fold remained (see the bar labeledwild type lsr). In contrast, S. typhimurium strains containing MudJinsertion mutations in lsrA, lsrC and lsrB were unable to eliminate AI-2from the culture fluids, as AI-2 activity equivalent to the inputactivity remained in the culture fluids after the incubation period. Inaddition, a strain containing an inframe deletion in lsrB is also unableto eliminate AI-2 from the supernatant in this assay (not shown). Theseresults indicate that a functional Lsr ABC transporter is required forthe process of removal of AI-2 from the medium. Presumably, inactivationof lsrD would result in a phenotype identical to that caused by mutationof lsrA, lsrC and lsrB, since we predict that LsrD is required to formthe channel along with LsrC. Unfortunately, we did not obtain a MudJinsertion in lsrD, so this was not tested.

However, lsrD mutants may be obtained using the MudJ insertion proceduredescribed herein, other transposon based mutagenesis procedures, geneticengineering techniques such as those described above (including sitedirected mutagenesis), chemical mutagenesis techniques or screens forisolating spontaneous mutants that are not responsive to AI-2. MudJinsertions in lsrF and lsrE did not impair the ability of S. typhimuriumto remove AI-2 from the medium. The figure shows that, similar to whenthe wild type lsr operon is present, 95% of the input activitydisappears after 1 h incubation in the lsrF and lsrE mutants. The lsrFand lsrE genes are located downstream of the genes encoding thestructural components of the transport apparatus (FIG. 17). Therefore,although the MudJ insertions generating lacZ transcriptional fusions tolsrE and lsrF are induced by AI-2 by virtue of their presence in the lsroperon, LsrE and LsrF are not expected to be required for building afunctional transport apparatus. Taken together, our results indicatethat only the genes that encode the structural components of the Lsrtransporter are required for removal of AI-2 from S. typhimuriumcell-free culture fluids.

FIG. 23 also shows that inactivation of lsrR results in the highestlevel of removal of AI-2 from the extracellular culture fluids of S.typhimurium, as over 99% of the activity is gone after the 1 hincubation. To verify that elimination of AI-2 from the medium that weobserved in this experiment depends on the Lsr transporter, we combinedthe ΔlsrR mutation with the lsrC::MudJ insertion and performed anidentical experiment. The final bar in FIG. 23 shows that regardless ofthe presence or absence of lsrR, inactivation of the Lsr transporterrenders S. typhimurium unable to eliminate AI-2 from the medium becausein the ΔlsrR, lsrC::MudJ double mutant, the level of AI-2 did notdecrease compared to the input activity.

Deletion of lsrR results in maximal removal of the AI-2 from the culturefluids. This result is expected because the ΔlsrR strain displayscompletely derepressed expression of the lsr operon, and this strainwould therefore be predicted to have increased levels of the Lsrtransporter compared to the wild type strain. If this is the case, theΔlsrR strain should have an enhanced capability to remove AI-2 from themedium. To test this idea, we assayed the rate of disappearance of AI-2from the medium over time for the ΔlsrR mutant and compared that to therate of disappearance for the wild type strain (FIG. 24). Thisexperiment shows that removal of AI-2 from the medium by the wild typelsrR strain occurs rather steadily over first 45 min of the incubationperiod, then more rapidly between 45 min and 1 h (triangles).Specifically 97, 85, 82, 75 and 6% of the input AI-2 activity remains at2, 15, 30, 45 and 60 min, respectively. In contrast, in the ΔlsrRmutant, only 10% of the AI-2 activity remains after 2 minutes, and allbut 2% of the activity is gone by 15 min (circles). This resultdemonstrates that the derepression of the expression of the Lsrtransport complex increases the efficiency of elimination of AI-2 fromthe external environment of S. typhimurium.

In our previous investigations of the model luminous bacterium V.harveyi, we identified a quorum sensing signal called AI-2, and showedthat it is involved in induction of the expression of luciferase(Bassler et al., 1993; Bassler et al., 1994a). Subsequently, we showedthat AI-2 and the synthase required for its production, LuxS, arepresent in a wide variety of bacterial species (Bassler et al., 1997;Bassler, 1999; Miller and Bassler, 2001; Surette et al., 1999). We havesuggested that AI-2 is used for inter-species communication amongbacteria (Bassler et al., 1997; Miller and Bassler, 2001; Surette etal., 1999). However, prior to the present invention, it was not clearhow AI-2 is detected nor what functions are regulated by this signal inmost species of bacteria. In the present application, we provide theresults of experiments aimed at identifying the AI-2 regulated genes andthe mechanism of AI-2 signal transduction in the enteric pathogen S.typhimurium.

The following description sets forth the general procedures involved inpracticing this aspect of the present invention. To the extent thatspecific materials are mentioned, it is merely for purposes ofillustration and is not intended to limit the invention. Unlessotherwise specified, general cloning procedures, such as those set forthin Sambrook et al., Molecular Cloning, Cold Spring Harbor Laboratory(1989) (hereinafter “Sambrook et al.”) or Ausubel et al. (eds) CurrentProtocols in Molecular Biology, John Wiley & Sons (1998) (hereinafter“Ausubel et al.”) are used.

EXAMPLE 1 Quorum Sensing in Escherichia coli and Salmonella typhimurium

There have been preliminary indications that E. coli senses cell density(Huisman et al., Science 265: 537-539, 1994; Sitnikov et al., Proc.Natl. Acad. Sci. USA 93: 336-341, 1996; Garcia-Lara et al., J.Bacteriol. 178: 2742-2748, 1996). We took advantage of the reducedselectivity of the Signaling System 2 sensor in V. harveyi to develop asensitive assay for detection of extracellular signal compounds producedby E. coli and S. typhimurium. Using this assay we could determine theconditions under which many strains of E. coli and S. typhimuriumsynthesize, secrete, and degrade a signaling substance that willinteract with the V. harveyi System 2 detector.

Materials and Methods

Preparation of cell-free culture fluids. E. coli strains AB1157 and DH5and S. typhimurium strain LT2 were grown at 30° C. overnight withaeration in LB broth containing glucose at the concentrations specifiedin the text. The following morning fresh LB medium containing the sameconcentration of glucose used for the overnight growth was inoculated ata 1:100 dilution with the over-night grown cultures. The fresh cultureswere grown for various times at 30° C. with aeration. Cell-free culturefluids were prepared by removing the cells from the growth medium bycentrifugation at 15,000 rpm for 5 min in a microcentrifuge. The clearedculture fluids were passed through 0.2 m HT Tuffryn filters (Gelman) andstored at −20° C. Cell-free culture fluids containing V. harveyiAutoin-ducer-2 were prepared from V. harveyi strain BB152 (Autoinducer1⁻, Autoinducer 2⁺). V. harveyi BB120 (Autoinducer 1⁺, Autoin-ducer 2⁺)was used to prepare culture fluids containing Autoinducer-1. In bothcases, the V. harveyi strains were grown overnight at 30° C. withaeration in AB (Autoinducer Bioassay) (Bassler et al., 1993, supra)medium. Cell-free culture fluids from V. harveyi were prepared from theovernight culture exactly as described above for E. coli and S.typhimurium.

Assay for production of signaling compounds. Cell-free culture fluidsfrom E. coli, S. typhimurium and V. harveyi strains were tested for thepresence of signaling substances that could induce luminescence in theV. harveyi reporter strain BB170 or BB886. In the assays, 10 μl ofcell-free culture fluids from E. coli AB1157, E. coli DH5, and S.typhimurium LT2 strains grown and harvested as described above wereadded to 96-well microtiter dishes. The V. harveyi reporter strain BB170or BB886 was grown for 16 h at 30° C. with aeration in AB medium,diluted 1:5000 into fresh AB medium, and 90 μl of the diluted cells wereadded to the wells containing the E. coli and S. typhimurium cell-freeculture fluids. Positive control wells contained 10 μl of cell-freeculture fluid from strain V. harveyi BB152 (Autoinducer-1⁻,Autoinducer-2⁺) or V. harveyi BB120 (Autoinducer-1⁺, Autoinducer-2⁺).Negative control wells contained 10 μl of sterile growth medium. Themicrotiter dishes were shaken in a rotary shaker at 175 rpm at 30° C.Every hour, light production was measured using a Wallac Model 1450Microbeta Plus liquid scintillation counter in the chemiluminescencemode. The V. harveyi cell density was measured by diluting the samealiquots of cells used for measuring luminescence, spreading thedilutions onto solid LM medium (Bassler et al., 1993, supra), incubatingthe plates overnight at 30° C., and counting the resulting colonies thefollowing day.

Preparation of E. coli and S. typhimurium viable and UV-killed cells forthe activity assay. E. coli AB1157, E. coli DH5 and S. typhimurium LT2cultures were grown for 8 h in LB containing 0.5% glucose at 30° C. withaeration. The cultures were subjected to centrifugation for 5 min at15,000 rpm in a microcentrifuge and the growth medium was removed fromthe cell pellets by aspiration. The cell pellets were resuspended in ABmedium and washed by vigorous mixing. The cells were again subjected tocentrifugation for 5 min at 15,000 rpm. The AB wash medium was removedand discarded and the cells were resuspended in fresh AB medium. Eachcell suspension was diluted to give 1×10⁶ cells/10 μl, and multiple 10μl aliquots were added to wells of microtiter dishes. Half of the cellaliquots were treated with short wavelength ultraviolet light for 15 minat a distance of 10 cm. This treatment was sufficient to kill all of thecells as judged by plating and incubating the UV-treated cells, andensuring that no growth occurred by the next day. 90 μl of the dilutedV. harveyi reporter strain BB170 was next added to the wells containingeither the viable or dead E. coli and S. typhimurium cells, and theactivity assay was carried out exactly as described in the previoussection.

Analysis of glucose in S. typhimurium LT2 culture fluids. Glucoseconcentrations were determined in cell-free culture fluids prepared fromS. typhimurium using a Trinder assay (Diagnostic Chemicals Ltd.)according to the recommendations of the manufacturer, except that theglucose standards were prepared in LB medium. The assay was sensitive toless than 0.002% glucose. No interfering substances were present in LBmedium or spent LB culture fluids.

Results and Discussion

E. coli AB1157 and S. typhimurium LT2 produce a signaling substance thatspecifically induces one of the two quorum sensing systems of V.harveyi. The V. harveyi reporter strain BB170 has the quorum sensingphenotype Sensor 1⁻, Sensor 2⁺. It induces lux expression in response toextracellular signals that act exclusively through the Signaling System2 detector. Addition of 10% cell-free spent culture fluid prepared fromV. harveyi strain BB152 (which contains the System 2 autoinducer)stimulates the reporter strain roughly 1000-fold over the endogenouslevel of luminescence expression. In FIG. 1, the light production by V.harveyi BB170 induced by the addition of 10% cell-free spent culturefluids is normalized to 100% activity.

E. coli strain AB1157 and S. typhimurium strain LT2 were grown for 8 hin LB broth or LB broth containing 0.5% glucose. The E. coli and S.typhimurium cells were removed from the growth medium and the cell-freeculture fluids were prepared and assayed for an activity that couldinduce luminescence expression in V. harveyi. Addition of 10% cell-freeculture fluid from S. typhimurium LT2 or E. coli AB1157 grown in LBcontaining glucose maximally induced luminescence in the reporter strainBB170, similar to culture fluids from V. harveyi BB152 (FIG. 1A).Specifically, E. coli AB1157 produced 106% and S. typhimurium produced237% of the V. harveyi BB152 activity. When the E. coli and S.typhimurium were grown in LB without added glucose they did not producethe signaling factor. Substitution of 10% (v/v) of LB medium containing0.5% glucose did not stimulate luminescence in the reporter strain,indicating that there is no substance in the LB-glucose growth mediumthat induces luminescence expression in V. harveyi. We tested obviouscandidates for the signal including glucose, amino acids, cAMP, acetate,homoserine lactone, -ketoglutarate and other keto acids that are knownto be excreted. None of these compounds has activity. These resultssuggest that V. harveyi BB170 can respond to some substance secreted byE. coli AB1157 and S. typhimurium LT2 when they are grown on LBcontaining glucose.

Analogous experiments were performed with the V. harveyi reporter strainBB886 (Sensor 1⁺, Sensor 2⁻). V. harveyi BB886 is defective in itsresponse to signaling compounds that act through the Signaling System 2detector, but it is an otherwise wild type strain (Bassler et al., Mol.Microbiol. 13: 273-286, 1994). FIG. 1B shows the normalized 100%activation of V. harveyi BB886 by cell-free spent culture fluidsprepared from V. harveyi BB120. V. harveyi BB120 produces the System 1autoinducer N-(3-hydroxybutanoyl)-L-homoserine lactone (Bassler et al.,1993, supra). Addition of S. typhimurium LT2 and E. coli AB1157cell-free culture fluids to V. harveyi strain BB886 caused a 5% and a 1%increase above the control level (FIG. 1B). Together the results of FIG.1 shows that the signaling compound produced by E. coli and S.typhimurium must act specifically through V. harveyi Signaling System 2and not some other, unidentified pathway.

Viable E. coli AB1157 and S. typhimurium LT2 are required for secretionof the signaling compound. We considered the possibility that growth ofE. coli AB1157 and S. typhimurium LT2 in LB medium containing glucosesimply allowed them to utilize and therefore remove some preexistinginhibitor of induction of luminescence. To show that the cellsthemselves produce the soluble signaling factor, we added washed E. coliand S. typhimurium cells directly to the luminescence assay. Theseresults are presented in FIG. 2. In this experiment, E. coli AB1157 andS. typhimurium LT2 were grown for 8 h in LB containing 0.5% glucose; theconditions for maximal production of the signaling factor. The cellswere removed from the LB-glucose growth medium by centrifugation, andsterile V. harveyi luminescence assay medium was used to wash andresuspend the cell pellets. 1×10⁶ E. coli AB1157 or S. typhimurium LT2cells were added to the diluted V. harveyi BB170 culture at the start ofthe experiment. In FIG. 2, the left-hand bar in each series shows thatthe presence of washed E. coli AB1157 or S. typhimurium LT2 cells issufficient to fully induce luminescence in V. harveyi BB170. E. coliAB1157 and S. typhimurium LT2 stimulated lux expression in V. harveyiBB170 821-fold and 766-fold respectively. Identical aliquots of thewashed E. coli or S. typhimurium cells were killed with short waveultraviolet light prior to addition to the assay. When dead cells wereincluded in the assay, no stimulation of luminescence occurred. In FIG.2, these results are shown in the right-hand bar for each strain. Takentogether, the results show that the stimulatory factor is produced bythe E. coli AB1157 and S. typhimurium LT2 cells themselves during thetime course of the experiment; the factor could not have come from themedium in which the cells had been grown. This factor is activelyreleased into the medium by E. coli and S. typhimurium because deadcells have no activity.

E. coli DH5 does not produce the signaling activity. Clinical isolatesof E. coli and Salmonella also produce the signaling compound. Tenclinical isolates of Salmonella and five pathogenic isolates of E. coliO157 were assayed and all produced the activity. It was conceivable thatthe signal was some normal byproduct of glucose metabolism that simplydiffuses out of the cells. This is not the case however, because we showthat E. coli DH5, which is equally capable of utilizing glucose as E.coli AB1157 and S. typhimurium LT2, does not produce the signalingactivity. FIG. 1A demonstrates that unlike E. coli AB1157 and S.typhimurium LT2, the addition of 10% cell-free culture fluid preparedfrom E. coli DH5 grown 8 h in LB containing 0.5% glucose does notstimulate light production in V. harveyi BB170. Similarly, inclusion ofwashed viable or killed E. coli DH5 cells in the luminescence assay doesnot stimulate V. harveyi BB170 to produce light (FIG. 2). The inabilityof E. coli DH5 to produce the activity indicates that this highlydomesticated strain lacks the gene or genes necessary for either theproduction or the export of the signaling activity. We assayed otherlaboratory strains of E. coli for the signaling activity (Table 1). OnlyE. coli DH5 was completely defective in producing the extracellularsignal.

Table 1. The induction of luminescence in V. harveyi reporter strainBB170 by cell-free culture fluids from V. harveyi, S. typhimurium and E.coli is shown. Cell-free culture fluids were prepared from variousstrains of V. harveyi, S. typhimurium and E. coli as described andtested for production of a signaling substance that could stimulatelight production in the reporter strain V. harveyi BB170. The level ofV. harveyi stimulation was normalized to 100%. The data for the 5 h timepoint are shown. TABLE 1 The induction of luminescence in V. harveyireporter strain BB170 by cell-free culture fluids from V. harveyi, S.typhimurium and E. coli is shown. Cell-free culture fluids were preparedfrom various strains of V. harveyi, S. typhimurium and E. coli asdescribed and tested for production of a signaling substance that couldstimulate light production in the reporter strain V. harveyi BB170. Thelevel of V. harveyi stimulation was normalized to 100%. The data for the5 h time point are shown. Species and Strain Induction of luminescence(%) V. harveyi V. harveyi BB152 100 Salmonella S. typhimurium LT2 237 E.coli E. coli AB1157 106 E. coli DH5 5 E. coli JM109 76 E. coli MG1655100 E. coli MC4100 93

Glucose regulates the production and degradation of the signaling factorby S. typhimurium LT2. Cell-free culture fluids from S. typhimurium LT2and E. coli AB1157 cells grown in LB without added glucose did notstimulate the expression of luminescence in the reporter strain,indicating that metabolism of glucose is necessary for the production ofthe signal. We tested other carbohydrates, and in general, growth in thepresence of PTS sugars (see Postma et al., in Escherichia coli andSalmonella Cellular and Molecular Biology, (F. C. Niehardt, ed), Am.Soc. Microbiol., Washington D.C., pp. 1149-1174, 1996) enabled E. coliAB1157 and S. typhimurium LT2 to produce the signal. Of the sugarstested, growth on glucose induced the synthesis of the highest level ofactivity. Growth on other carbon sources, for example TCA cycleintermediates and glycerol, did not induce significant production of thesignaling activity.

We tested whether the presence of glucose was required for the cells tocontinue to produce the signal. FIG. 3 shows results with S. typhimuriumLT2 grown in LB containing limiting (0.1%) and nonlimiting (0.5%)glucose concentrations. FIG. 3A shows that when glucose is limiting, S.typhimurium LT2 produces the signal in mid-exponential phase (after 4 hgrowth), but stops producing the signaling activity once glucose isdepleted from the medium. FIG. 3B shows that when glucose does notbecome limiting, S. typhimurium LT2 produces greater total activity andcontinues to produce the signaling activity throughout exponentialphase, with maximal activity at 6 h growth. Furthermore, the Figure alsoshows that the signaling activity synthesized by midexponential phasecells is degraded by the time the cells reach stationary phase. Inconditions of limiting glucose, no activity remained at stationaryphase, and when glucose was plentiful, only 24% of the activityremained. Increasing the concentration of glucose in the growth mediumdid not change these results, i.e., the activity was secreted duringmidexponential growth and severely reduced activity remained in thespent culture fluids by stationary phase.

In sum, the results presented in this example show that E. coli and S.typhimurium produce a signaling substance that stimulates one specificquorum sensing system in V. harveyi. Many other bacteria have previouslybeen assayed for such an activity, and only rarely were speciesidentified that are positive for production of this factor (Bassler etal., 1997, supra). Furthermore, as shown here, the E. coli and S.typhimurium signal is potent, these bacteria make activity equal to thatof V. harveyi. The degradation of the E. coli and S. typhimurium signalprior to stationary phase indicates that quorum sensing in thesebacteria is tuned to low cell densities, suggesting that quorum sensingin E. coli and S. typhimurium is modulated so that the response to thesignal does not persist into stationary phase. Additionally, quorumsensing in E. coli and S. typhimurium is influenced by severalenvironmental factors. The production and the degradation of the signalare sensitive not only to growth phase but also to the metabolicactivity of the cells. These results indicate that the quorum sensingsignal in E. coli and S. typhimurium has two functions; it allows thecells to communicate to one another their growth phase and also themetabolic potential of the environment.

Understanding the regulation of quorum sensing in E. coli and S.typhimurium is important for understanding community structure andcell-cell interactions in pathogenesis. In the wild, pathogenic E. coliand S. typhimurium may never reach stationary phase because dispersionis critical. It is therefore appropriate that quorum sensing in E. coliand S. typhimurium should be functioning at low cell density. Thissituation is in contrast to that of V. fischeri, the luminescent marinesymbiont, where the quorum sensing system is only operational at highcell densities; cell densities indicative of existence inside thespecialized light organ of the host. The specific quorum sensing systemsof V. fischeri and E. coli and S. typhimurium appear appropriatelyregulated for the niche in which each organism exists. In both cases,quorum sensing could be useful for communicating that the bacteriareside in the host, not free-living in the environment. Additionalcomplexity exists in the E. coli and S. typhimurium systems becausethese bacteria channel both cell density information and metabolic cuesinto the quorum sensing circuit. Again, signals relaying informationregarding the abundance of glucose or other metabolites couldcommunicate to the bacteria that they should undergo the transition froma free-living mode to the mode of existence inside the host.

Under all the conditions we have tested, the signaling activitydescribed in this example does not extract quantitatively into organicsolvents and it does not bind to either a cation or anion exchangecolumn. Preliminary characterization indicates that the signal is asmall (less than 1000 MW) polar but apparently uncharged organiccompound. The activity is acid stabile and base labile, it is heatresistant to 80 but not 100° C. Purification of the E. coli, S.typhimurium and V. harveyi signal is described in greater detail in thefollowing examples.

EXAMPLE 2 Regulation of Autoinducer Production in Salmonella typhimurium

In this example, the conditions under which S. typhimurium LT2 producesAI-2, the extracellular factor that stimulates lux expression in the V.harveyi Sensor 1⁻, Sensor 2⁺ reporter strain, are elucidated. Productionof the signaling compound by S. typhimurium occurs during growth onpreferred carbohydrates that, upon utilization by the bacteria, resultin a decrease in the pH of the medium. Lowering the pH of the growthmedium in the absence of a preferred carbon source induces limitedproduction of the factor, indicating that the cells are influenced byboth the changing pH and the utilization of the carbon source. Thesignaling activity is degraded by the time the cells reach stationaryphase, and protein synthesis is required for degradation of theactivity. Osmotic shock following growth on an appropriate carbon sourcegreatly increases the amount of activity present in the S. typhimuriumculture fluids. This increased activity is apparently due to inductionof synthesis of the autoinducer and repression of degradation of theactivity. E. coli and S. typhimurium possess a protein called SdiA thatis homologous to LuxR from V. fischeri (Wang et al., EMBO J. 10:3363-3372, 1991; Ahmer et al., J. Bacteriol. 180: 1185-1193, 1998). SdiAis proposed to respond to an extracellular factor (Sitnikov et al.,Proc. Natl. Acad. Sci. USA 93: 336-341, 1996; Garcia-Lara et al., J.Bacteriol. 178: 2742-2748, 1996), and it has been shown to controlvirulence factor production in S. typhimurium (Ahmer et al., 1998,supra). The analysis set forth below shows that the AI-2 autoinducersignaling activity does not function through the SdiA pathway.

Material and Methods

Strains and Media. The bacterial strains used in this study and theirgenotypes and phenotypes are listed in Table 2. TABLE 2 Bacterialstrains; their genotypes and relevant phenotypes. Strain GenotypeRelevant Phenotype S. typhimurium LT2 Wild type E. coli O157 Wild typeE. coli MG1655 F⁻, ilvG, rfb-50 Wild type E. coli MC4100 (lac)U169,araD139, rpsL, thi LacZ⁻ E. coli DH5 supE44, hsdR17, recA1, AI-2⁻ endA1,gyrA96, thi-1, relA1 V. harveyi BB170 luxN::Tn5 Sensor 1⁻, Sensor 2⁺ V.harveyi BB152 luxL::Tn5 AI-1⁻, AI-2⁺ V. harveyi JAF305 luxN::Cm^(r)Sensor 1⁻, Sensor 2⁺

Luria broth (LB) contained 10 g Bacto Tryptone (Difco), 5 g YeastExtract (Difco) and 10 g NaCl per liter (Sambrook et al., 1989). Therecipe for Autoinducer Bioassay (AB) medium has been reported previously(Greenberg et al., Arch. Microbiol. 120: 87-91, 1979). LM medium(L-Marine) contains 20 g NaCl, 10 g Bacto Tryptone, 5 g Bacto YeastExtract and 15 g Agar per liter (Bassler et al., 1994, supra).Regulation of AI-2 production similar to that reported here was alsoobserved with the ATCC strain Salmonella enterica Serovar Typhimurium14028, an independent clinical isolate of Salmonella enterica SerovarTyphimurium, and nine other Salmonella enterica serovars (other thanTyphimurium).

Growth conditions for S. typhimurium LT2 and preparation of cell-freeculture fluids. S. typhimurium LT2 was grown overnight in LB broth withshaking at 30° C. The next day, 30 μl of the overnight culture was usedto inoculate 3 ml of fresh LB broth. In cultures containing additionalcarbon sources, at the time of inoculation, 20% sterile stock solutionswere added to give the specified final concentrations. Followingsubculturing of the cells, the tubes were shaken at 200 rpm at 30° C.for the time periods indicated in the text. Cell-free culture fluidswere prepared by removal of the cells from the culture medium bycentrifugation for 5 min at 15,000 rpm in a microcentrifuge. The clearedsupernatants were passed through 0.2 m cellulose acetate Spin X filters(CoStar, Cambridge, Mass.) by centrifugation for 1 min at 8000×g.Samples were stored at −20° C. Similar results to those reported herewere obtained when we grew the S. typhimurium at 37° C. The preparationof cell-free culture fluids from V. harveyi strains has already beenreported (Bassler et al., 1993, supra; Bassler et al., 1997, supra).

Density-dependent bioluminescence assay. The V. harveyi reporter strainBB170 (Sensor 1⁻, Sensor 2⁺) (Bassler et al., 1993, supra) was grown for12 h at 30° C. in AB medium, and diluted 1:5000 into fresh AB medium.Luminescence was measured as a function of cell density by quantitatinglight production at different times during growth with a Wallac Model1409 liquid scintillation counter (Wallac Inc., Gaithersburg, Md.). Thecell density was measured by diluting the same aliquots of cells usedfor measuring luminescence, spreading the dilutions onto solid LMmedium, incubating the plates overnight at 30° C., and counting theresulting colonies the following day. Relative Light Units are (countsmin⁻¹ ml−1×10³)/(colony forming units ml⁻¹). Cell-free culturesupernatants from V. harveyi or S. typhimurium strains were added to afinal concentration of 10% (v/v) at the time of the first measurement.In control experiments, 10% (v/v) of AB medium, LB medium or LB mediumcontaining 0.5% glucose was added instead of cell-free culture fluids.

S. typhimurium autoinducer activity assay. The quorum sensing signalingactivity released by S. typhimurium LT2 was assayed following growthunder various conditions. 10 10 μl of cell-free culture fluids from S.typhimurium LT2 grown and harvested as described above were added to96-well microtiter dishes. The V. harveyi reporter strain BB170 wasgrown overnight and diluted as described above. 90 μl of the diluted V.harveyi cells were added to the wells containing the S. typhimuriumcell-free culture fluids. Positive control wells contained 10 μl ofcell-free culture fluid from V. harveyi BB152 (AI-1⁻, AI-2⁺) (Bassler etal., 1993, supra). The microtiter dishes were shaken in a rotary shakerat 200 rpm at 30° C. Light production was measured hourly using a WallacModel 1450 Microbeta Plus liquid scintillation counter designed formicrotiter dishes (Wallac Inc., Gaithersburg, Md.). In theseexperiments, the cell density was not measured at each time point.Rather, to ensure that increased light production was due to a signalingactivity and not a growth medium component, the luminescence productionby V. harveyi in wells containing cell-free culture fluids was comparedto that produced by V. harveyi in wells containing 10 μl of theidentical growth medium alone. Data are reported as fold-stimulationover that obtained for growth medium alone.

Factors controlling signal production in S. typhimurium. S. typhimuriumLT2 was grown for 6 h in LB containing 0.5% glucose as described above.The mid-exponential phase culture was divided into several identicalaliquots. One aliquot of cells was grown to stationary phase (24 h at30° C. with shaking). In the remaining aliquots, the cells were removedfrom the LB-glucose growth medium by centrifugation for 5 min at 15,000rpm in a microcentrifuge. The resulting cell pellets were resuspended atan OD₆₀₀ of 2.0 in either LB, LB+0.5% glucose, LB at pH 5.0, or in 0.1 MNaCl, or 0.4 M NaCl (in water). The resuspended cells were shaken at 30°C. or 43° C. for 2 h. Cell-free fluids were prepared from the stationaryphase culture, and from the cells that had been resuspended andincubated in the various media or the osmotic shock solutions. Thecell-free fluids were tested for signaling activity in the S.typhimurium activity assay as described above.

Effects of growth phase, pH, glucose concentration and osmolarity onautoinducer production by S. typhimurium. S. typhimurium LT2 was grownat 30° C. for various times in LB containing limiting (0.1%) andnon-limiting (1.0%) glucose concentrations. At the times specified inthe text, the cell number was determined by plating dilutions of the S.typhimurium cultures onto LB medium and counting colonies the followingday. The pH of the two cultures was measured, and the percent glucoseremaining in each culture was determined using the Trinder assay asdescribed in Example 1. Cell-free culture fluids were prepared from theLB-glucose cultures as described above. The same cells from which thecell-free culture fluids were prepared were resuspended in 0.4 M NaClosmotic shock solution and shaken at 200 rpm, 30° C. for 2 h. Wedetermined that this timing was optimal for production of autoinducer.The cells were removed from the osmotic shock solution by centrifugationat 15,000 rpm for 5 min in a microcentrifuge. Cell-free osmotic shockfluids were prepared from the resuspended cells exactly as described forcell-free culture fluids. Signaling activity in both the cell-freeculture fluids and the cell-free osmotic shock fluids was assayed asdescribed above. In experiments in which the pH was maintained at 7.2,the cells were grown in LB+0.5% glucose containing 50 mM MOPS at pH 7.2.The pH was adjusted every 15-30 min using I M MOPS pH 7.2. Inexperiments performed at pH 5.0, LB broth was maintained between pH 5.0and 5.2 with 1 M NaOH.

Requirement for protein synthesis in signal production, release anddegradation by S. typhimurium LT2. S. typhimurium LT2 was pregrown in LBcontaining 0.5% glucose at 30° C. to an OD₆₀₀ of 2.5 (approximately 6-8h). The culture was divided into four identical aliquots. Two aliquotswere treated with 100 g/ml Cm for 5 min at room temperature after whichthe cells were harvested by centrifugation at 15,000 rpm for 5 min. OneCm-treated cell pellet was resuspended in 0.1 M NaCl containing 30 g/mlCm, and the second pellet was resuspended in 0.4 M NaCl containing 30g/ml Cm. Each of these pellets was resuspended to a final OD₆₀₀ of 2.0.The remaining two culture aliquots were not treated with Cm. Instead,the cells in these two aliquots were harvested by centrifugation andresuspended in 0.1 M and 0.4 M NaCl exactly as described for theCm-treated cells. The cell suspensions were incubated at 30° C. withshaking. At the times indicated in the text, 1.5 ml aliquots wereremoved from the cell suspensions and cell-free osmotic shock fluidswere prepared by the procedure described above.

Analysis of the effect of autoinducer on SdiA regulated gene expression.A sequence that includes the ftsQ1p and ftsQ2p promoters (Wang et al.,1991, supra) was amplified from E. coli MG1655 chromosomal DNA using thefollowing primers: (SEQ ID NO: 19) ftsQ1p,5′-CGGAGATCTGCGTTTCAATGGATAAACTACG-3′; (SEQ ID NO: 20) ftsQ2p,5′-CGCGGATCCTCTTCTTCGCTGTTTCGCGTGT-3′.

The amplified product contained both the ftsQ promoters and the first 14codons of the ftsQ gene flanked by BamHI and BglII sites. The ftsQ1p2pPCR product was cloned into the BamHI site of vector pMLB1034 (Silhavyet al., Experiments with Gene Fusions, Cold Spring Harbor Press, 1984)to generate a lacZ fusion that contained the promoters, ribosome bindingsite, and initiation codon of ftsQ. A correctly oriented clone, pMS207,and a clone containing the ftsQ1p2p insert in the opposite orientation,pMS209, were chosen for further analysis. Both inserts were sequenced toensure that no errors were introduced during the PCR reaction.

For ftsQ regulation in E. coli, the plasmids pMS207 and pMS209 weretransformed into E. coli strain MC4100 (Silhavy et al., 1984, supra),and the transformants were grown overnight in LB containing 100 mg/Lampicillin at 30° C. with aeration. For rck regulation, S. typhimuriumstrains BA1105 (rck::MudJ) and BA1305 (rck::MudJ sdiA) were grownovernight in LB containing 100 mg/L kanamycin at 30° C. with aeration.The overnight cultures were diluted 20-fold into fresh medium and grownfor an additional 4.5 h. At this time, each culture was divided intofive identical aliquots and 10% (v/v) of one of the following was addedto each aliquot: LB, 0.4 M NaCl, 0.4 M osmotic shock fluids from S.typhimurium LT2, E. coli O157 or E. coli strain DH5 (negative control).The osmotic shock fluids were prepared as described above, followingpregrowth of the S. typhimurium LT2 and E. coli in LB containing 0.5%glucose for 6 h. The cell suspensions were incubated at 30° C. for 2 h,after which standard -galactosidase reactions were performed on thesamples (Miller, A Short Course in Bacterial Genetics, Cold SpringHarbor Laboratory Press, 1992).

Results

S. typhimurium LT2 produces an autoinducer-like activity. In Example 1it was demonstrated that S. typhimurium and E. coli strains produce asignaling activity that stimulates lux expression in V. harveyi, and thesignaling compound acts exclusively through the V. harveyi quorumsensing System 2. FIG. 4 shows the induction of luminescence in the V.harveyi System 2 reporter strain BB170 (Sensor 1⁻, Sensor 2⁺). Thecharacteristic quorum sensing behavior of V. harveyi is shown in thecontrol experiment (closed circles). Immediately after dilution intofresh medium, the light emitted per cell by V. harveyi drops rapidly,over 1000-fold. At a critical cell density, which corresponds to theaccumulation of a critical concentration of endogenously producedautoinducer (AI-2) in the medium, the luminescence per cell increasesexponentially, approximately 3 orders of magnitude, to again reach thepredilution level.

Addition of 10% cell-free culture fluid prepared from V. harveyi BB152(AI-1⁻, AI-2⁺) caused the reporter strain to maintain a high level oflight output following dilution (open circles). The increased lightoutput is due to the V. harveyi BB170 cells responding to the presenceof AI-2 in the cell-free culture fluids prepared from V. harveyi strainBB152 (Bassler et al., 1993, supra). Similarly, addition of cell-freeculture fluid from S. typhimurium LT2 grown in LB+0.5% glucose inducedluminescence in the reporter strain approximately 800-fold over thecontrol level (solid squares). No activity similar to V. harveyi AI-1was produced by S. typhimurium LT2 under these conditions and there isno AI-1 or AI-2 activity in LB+0.5% glucose (see Example 1).

Environmental factors influence autoinducer production and degradationin S. typhimurium. Control of autoinducer production in S. typhimuriumis different than in other described quorum sensing systems. FIG. 5Ademonstrates three important aspects of the regulation of autoinducerproduction in S. typhimurium. First, no autoinducer activity is observedwhen S. typhimurium is grown for 6 h in LB in the absence of glucose.Second, growth in the presence of glucose for 6 h results in substantialproduction of autoinducer (760-fold activation of the reporter strain).Third, activity, while detectable, is severely reduced when the S.typhimurium culture is allowed to grow to stationary phase (33-foldactivation of the reporter strain).

We subjected S. typhimurium LT2 to several different treatmentsincluding some enviromnental stresses in order to begin to understandwhat conditions favor autoinducer production versus those that favorautoinducer degradation. In the experiment presented in FIG. 5B, the S.typhimurium cells were induced for signal production by pregrowth in LBcontaining 0.5% glucose for 6 h. We have shown that under theseconditions, the glucose is not depleted (Surette and Bassler, 1998).After the induction phase of growth, the culture fluid was removed andaliquots of the cells were resuspended and incubated for 2 h under avariety of conditions that are described in the description of FIG. 2.Following each of these treatments cell-free fluids were prepared andtested for activity on BB170.

It is important to note that in the results presented in FIG. 5B, the S.typhimurium were pre-induced for autoinducer production at the start ofthe experiment, i.e., their cell-free culture fluid activated thereporter strain 760-fold. FIG. 5B shows that removal of the pre-growthculture fluid from these cells and resuspension of the cells in LBwithout glucose, in 0.1 M NaCl (hypotonic conditions), or heat shock at43° C. for 2 h resulted in no or very low autoinducer production. Theseresults indicate that the above treatments result in termination ofautoinducer production, or degradation of newly released autoinducer, orboth.

In contrast to the above results, resuspension of pre-induced cells infresh LB+glucose resulted in continued high-level production ofautoinducer (735-fold activation of the reporter). Similarly, acidic pHpromoted continued production of autoinducer (600-fold activation), andhypertonic osmotic shock (0.4 M NaCl) resulted in 1300-fold induction ofthe reporter. Increased AI-2 activity was only observed in the pH 5.0fluids or 0.4 M NaCl osmotic shock fluids of cells that were alreadyactively producing AI-2, i.e., if glucose was not included during thepre-growth, no measurable activity was produced following the identical2 h treatments.

Shifting S. typhimurium cells from LB+glucose to 0.4 M NaCl resulted inan accumulation of AI-2 activity to a level much greater than thatobserved under any other condition tested. Below it is shown that S.typhimurium cells resuspended in 0.4 M NaCl increase the biosynthesisand/or release of autoinducer, and furthermore they apparently do notdegrade significant quantities of the released activity. A similarincrease in AI-2 production occurs when the S. typhimurium cells areresuspended in 0.4 M NaCl, 0.4 M KCl or 0.8M sucrose, indicating thatthe NaCl effect on AI-2 production is an osmotic one, not an ionic one.This apparent osmotic shock effect on the S. typhimurium cells wasextremely useful because it enabled us to measure maximal release ofautoinducer activity in the absence of loss due to degradation.

The effect of glucose on signal production in S. typhimurium. In Example1 we showed that the continued presence of glucose was required for S.typhimurium to produce the quorum sensing signaling factor. Becausesugar utilization both increases the growth rate while decreasing the pHof the culture, we further analyzed the effect of metabolism of glucose,decreasing pH and increasing cell number on signal production by S.typhimurium. In the experiment presented in FIG. 6, we measured signalproduction, growth rate, and pH in growing S. typhimurium LT2 culturescontaining limiting (0.1%) and nonlimiting (1.0%) concentrations ofglucose. In the data presented in FIG. 6, at various times, the level ofautoinducer produced in both the cell-free culture fluids and in thecorresponding 0.4 M NaCl osmotic shock fluids was measured andnormalized for 1×10⁹ cells. It should be noted that unlike in FIG. 5,the cells in this experiment were not pre-induced for signal production.

FIG. 6 shows that the pattern of production and disappearance ofautoinducer observed in 0.4 M NaCl osmotic shock fluids mimics thatobserved in cell-free culture fluids. However, at every time point thatautoinducer is produced, much greater activity is detected in theosmotic shock fluids than in the corresponding cell-free culture fluids.Under conditions of limiting (0.1%) glucose (FIGS. 6A, 6C and 6E), S.typhimurium produces the signaling activity between 2-4 h (Bars).However, the glucose becomes completely depleted at 4 h, and at thattime production of the factor ceases (FIG. 6A). In contrast, when thecells are grown in 1.0% glucose (FIGS. 6B, 6D, and 6F), glucose ispresent in the medium throughout the entire experiment (FIG. 6B). Underthese conditions, the cells continue to synthesize activity for 12hours. Similar to the results shown in FIG. 5 and those reported inExample 1, almost no activity was observed in cell-free culture fluidsor osmotic shock fluids from stationary phase cells at 24 h regardlessof the glucose concentration.

S. typhimurium grows at roughly the same rate in both high and lowglucose media during exponential phase. In fact, the S. typhimuriumculture grown in high glucose medium does not reach the cell densityachieved by the S. typhimurium grown in the low glucose medium (FIGS. 6Cand 6D). Cell growth is probably inhibited in this culture by thedramatically reduced pH that occurs from increased glucose utilization.These results show that the higher level of activity produced by S.typhimurium in the LB containing 1% glucose is not due to higher cellnumber, but due to induction of signal production caused by glucosemetabolism.

FIGS. 6E and 6F show the pH of the low and high glucose cultures at eachtime point. Under conditions of low glucose (FIG. 6E), the pH of theculture initially decreases as the cells utilize the glucose. However,simultaneous to the complete depletion of the glucose, the pH begins torise. In contrast, under conditions of high glucose, the pH of themedium decreases to below pH 5 (FIG. 6F). In the experiments presentedin FIG. 6, both glucose catabolism and decreasing pH occursimultaneously suggesting that either or both of these factors could beresponsible for signal production by S. typhimurium.

Both glucose metabolism and low pH independently control signalproduction in S. typhimurium. To distinguish between the contributionfrom glucose metabolism and that from low pH in signal production by S.typhimurium, we compared the activity produced by S. typhimurium grownin LB containing 0.5% glucose in a culture in which the pH wasmaintained at 7.2 (FIG. 7A), to that produced by S. typhimurium grown inLB without glucose where the pH was maintained at 5.0 (FIG. 7B). Again,we measured the signal present in cell-free culture fluids and in 0.4 MNaCl osmotic shock fluids. Similar to the data presented in FIG. 3, thelevel of signal observed in cell-free culture fluids was lower than thatobserved in the 0.4 M osmotic shock fluids.

When S. typhimurium was grown in LB+0.5% glucose at pH 7.2 increasingamounts of the quorum sensing signal were detected for 6 h. At 6 h, in0.4 M NaCl osmotic shock fluids, there was an approximately 550-foldstimulation of light production of the V. harveyi reporter strain BBI70. No activity was produced after the 6 h time point. FIG. 7A showsthat the pH was maintained between 7.15 and 7.25 for 8 h, after thistime, the pH of the culture no longer decreased, but began increasingpresumably because the cells had depleted the glucose. We allowed the pHto continue to increase for the duration of the experiment. Also shownin the Figure is the cell number at each time point. At pH 7.2, thecells grew rapidly and reached a high cell density.

Analysis of time courses similar to those presented here, has shown thatS. typhimurium does not produce any signal when it is grown in LBwithout glucose at neutral pH (see Example 1). However, S. typhimuriumdid transiently produce the quorum sensing factor in the absence ofglucose when grown at pH 5.0 (FIG. 7B). Signal was produced for 4 h, andabout 450-fold stimulation of the reporter was the maximum activityachieved in 0.4 M NaCl osmotic shock fluids. Very little signal wasproduced by 5 h, and signal was completely absent after 6 h ofincubation. FIG. 7B shows that the pH was maintained between 5.0 and 5.2in this experiment. Note that the cells grew much more slowly at pH 5.0than at pH 7.2.

Preliminary characterization of the S. typhimurium autoinducerdegradative apparatus. The quorum sensing activity produced by S.typhimurium LT2 is degraded by the onset of stationary phase. We havedetermined that the activity contained in cell-free culture supernatantsand 0.4 M NaCl osmotic shock fluids from cells grown for 6 h inLB+glucose is stable for at least 24 h at 30° C., indicating that nodegradative activity is present in these cell-free fluids. Furthermore,mixing cell-free culture fluids prepared from actively producing S.typhimurium (i.e., from cultures grown for 6 h in LB+glucose) withcell-free culture fluids prepared from S. typhimurium that have degradedthe factor (i.e., from cultures grown for 12 or 24 h in LB+glucose) doesnot result in degradation of the activity. This result indicates thatthe degradative activity is not released, but instead, is associatedwith the cells.

We show in FIG. 5 that no further autoinducer is produced if S.typhimurium cells that are actively releasing autoinducer are shifted to0.1 M NaCl. However, when these same cells are shifted to 0.4 M NaCl, weobserve even greater autoinducer production. This result implies thatlow osmolarity could be a signal that induces the autoinducerdegradative machinery. To begin to analyze the mechanism by whichosmolarity affects autoinducer production and degradation in S.typhimurium, we investigated the requirement for protein synthesis insignal production and degradation by S. typhimurium in high and lowosmolarity. As described in the legend to FIG. 5, S. typhimurium LT2 wasgrown in LB containing 0.5% glucose to achieve maximal induction ofsignal production then treated with 0.1 M or 0.4 M NaCl in the presenceand absence of protein synthesis. Cell-free fluids were prepared andtested for signaling activity. Because half of the cell-free osmoticshock fluids contained chloramphenicol (Cm), V. harveyi JAF305 was usedas the reporter strain in the activity assay. This V. harveyi straincontains a Cm^(r) cassette in the luxN gene, and its phenotype is Sensor1⁻, Sensor 2⁺, a phenotype identical to that of V. harveyi BB170.

When the cells were resuspended in 0.4 M NaCl, the S. typhimuriumproduced and released increasing amounts of the signal for 200 min (FIG.8A, open squares). After this time, the level of signaling activitypresent in the cell-free osmotic shock fluid decreased somewhat,suggesting that some of the released signal was degraded. Quitedifferent results were obtained when the S. typhimurium cells wereresuspended in 0.1 M NaCl (FIG. 8B, open squares). In this case, atearly time points, the S. typhimurium produced a quantity of activityequivalent to that produced by cells resuspended in 0.4 M NaCl. However,by 120 min, no activity remained in the cell-free low osmolarity fluid.This result indicates that under conditions of low osmolarity, thereleased activity is rapidly degraded. We do not observe degradation ofthe activity in cell-free culture fluids, indicating that thedisappearance of the activity from low osmolarity cell-free fluids isnot due to chemical instability of the signaling compound.

Under conditions of high osmolarity, when the cells were treated with Cmto inhibit protein synthesis, only about one quarter of the activity wasproduced compared to untreated cells. The closed squares in FIG. 8A showthat 300-fold induction of the reporter strain occurred in the presenceof Cm as compared to 1200-fold induction with the untreated cells (FIG.8A, open squares). When the S. typhimurium was resuspended in lowosmolarity (FIG. 8B), roughly three-quarters of the activity produced inthe absence of Cm (open squares) was produced in the presence of Cm(closed squares). In the presence of Cm, the released activity was notdegraded by 300 min in high osmolarity and only partially degraded inlow osmolarity.

To show that high osmolarity does not inhibit AI-2 signal degradation,we added the activity contained in the 0.4 M NaCl cell-free osmoticshock fluids to S. typhimurium cells that had been resuspended in 0.1 MNaCl for two hours. As shown in FIG. 8, these are cells that can degradethe factor. Table 3 shows that these S. typhimurium cells degradedgreater than 98% of the signaling activity while incubated at highosmolarity. The table also shows that S. typhimurium cells that had beenincubated in 0.4 M NaCl (these are cells that are actively producing thesignal) released no further activity when resuspended in the 0.1 M NaClincubation fluid obtained from the actively degrading cells.Furthermore, mixing active and inactive 0.4 M and 0.1 M cell-freeosmotic fluids did not result in degradation of the activity in the 0.4M fluids. TABLE 3 High osmolarity induces release and low osmolarityinduces degradation of the S. Typhimurium signaling factor. TreatmentFold-induction of luminescence 0.1 M NaCl activity^(a) 4 0.4 M NaClactivity^(a) 944 0.1 M cells + 0.4 M activity^(b) 17 0.4 M cells + 0.1 Mactivity^(c) 6

^(a) S. typhimurium was grown for 6 h in LB containing 0.5% glucose. Thecells were pelleted and resuspended in either 0.1 M or 0.4 M NaCl for 2h. Cell-free fluids were prepared and tested for activity.

^(b) S. typhimurium cells that had been incubated in 0.1 M NaCl for twohours were pelleted and resuspended in the activity contained in thecleared osmotic shock fluids obtained from cells suspended in 0.4 M NaClfor 2 h. Cell-free fluids were prepared after a 2 h incubation andassayed for signaling activity.

^(c) S. typhimurium cells that had been suspended in 0.4 M NaCl werepelleted and incubated for 2 h in the cleared osmotic shock fluidsobtained from cells suspended for 2 h in 0.1 M NaCl. Cell-free fluidswere prepared after the 2 h incubation and assayed for signalingactivity.

The LuxR homolog SdiA is not involved in response to the AI-2autoinducer. A gene homologous to luxR of V. fischeri has beenidentified in E. coli and S. typhimurium and is called sdiA. Two reportssuggest that in E. coli, SdiA modestly regulates the expression of thecell division locus ftsQAZ in response to a factor present in cell-freeculture fluids (Garcia-Lara et al., 1996, supra), and in response to afew homoserine lactone autoinducers (Sitnikov, et al., 1996, supra).Completion of the sequence of the E. coli genome shows that no LuxIhomologue exists in E. coli so the locus responsible for thebiosynthesis of the hypothesized soluble factor(s) has not beendetermined. Overexpression of SdiA in S. typhimurium has recently beenshown to influence the expression of several ORFs located on the S.typhimurium virulence plasmid (Ahmer, et al., 1998, supra). As in the E.coli studies, SdiA activity in S. typhimurium is proposed to bemodulated by an extracellular factor.

It was possible that the AI-2 autoinducer that we have beencharacterizing in S. typhimurium and E. coli acted through SdiA. Wetested whether AI-2 had an effect on genes regulated by SdiA in E. coliand S. typhimurium. In E. coli, we assayed an ftsQ1p2p-lacZ reporter,and in S. typhimurium we assayed an rck::MudJ fusion in both an sdiA+andsdiA⁻ background. We tested the effects of addition of LB, 0.4 M NaCl,0.4 M NaCl osmotic shock fluids containing AI-2 activity from S.typhimurium LT2, E. coli O157, and 0.4 M NaCl osmotic shock fluid fromE. coli DH5. We have shown previously in Example 1 that DH5 does notproduce AI-2 activity under our growth conditions.

For the E. coli experiments we determined that MC4100 and MC4100/pMS209(containing ftsQ1p2p in the incorrect orientation) had nomeasurable-galactosidase activity. The level of -galactosidase producedby MC4100/pMS207 (containing the ftsQ1p2p-lacZ fusion) was roughly 20-30Miller units, and this level of activity did not change under any of theconditions tested here. This level of activity of the fusion wascomparable to that reported previously (Sitnikov et al., 1996, supra;Garcia-Lara et al., 1996, supra). In the S. typhimurium SdiA studies,similar to Ahmer et al. (1998, supra), we obtained ˜30 Miller units ofrck::MudJ activity in the sdiA⁺ background and this level was reduced to10 units in the sdiA⁻ background. No change in -galactosidase productionoccurred following the addition of AI-2 from E. coli or S. typhimurium.These results indicate that, if an extracellular factor exists thatmodulates the activity of SdiA, under the conditions we have tested, itis not AI-2.

Discussion

Quorum Sensing in E. coli and S. typhimurium. We have developed aheterologous bioassay that enables us to detect an extra-cellularsignaling factor produced by S. typhimurium. The factor mimics theaction of AI-2 of the quorum sensing bacterium V. harveyi, and it actsspecifically through the V. harveyi Signaling System 2 detector LuxQ.Results using lacZ fusions to the ftsQ and rck promoters indicate that,under our assay conditions, the AI-2 quorum sensing factor does notsignal to SdiA, at least with respect to regulation of these genes. TheAI-2 quorum sensing system is therefore involved in a different S.typhimurium and E. coli signal transduction pathway than the one(s)investigated previously.

S. typhimurium LT2 produces an amount of activity roughly equivalent tothat produced by V. harveyi. We observe approximately 800-foldstimulation of the V. harveyi reporter strain BB170 upon addition of 10%S. typhimurium cell-free culture fluids. The timing of lux induction andthe shape of the response curve of V. harveyi to the S. typhimuriumsignal are indistinguishable from those of V. harveyi responding to itsown AI-2. Furthermore, we have been successful at partially purifyingboth the V. harveyi AI-2 and the S. typhimurium signal compound usingidentical purification procedures. These two results lead us to believethat the S. typhimurium signaling compound is identical to or veryclosely related to AI-2 of V. harveyi.

Growth Conditions Regulate Signal Production and Degradation in S.typhimurium. In this example, we further characterize the regulation ofthe signaling activity in S. typhimurium LT2. Accumulation of signalingactivity in S. typhimurium culture supernatants is maximal duringmid-exponential phase when the cells are actively utilizing glucose inrich medium. Under these growth conditions, utilization of glucose isaccompanied by a rapid drop in pH of the culture. The resultsdemonstrate that either glucose metabolism or low pH is sufficient toinduce S. typhimurium LT2 to produce the quorum sensing factor,indicating that both glucose and acidity generate independent signalsfor autoinducer production. In the presence of glucose, when the pH isnot maintained, probably both the decreasing pH and the presence of anappropriate carbon source contribute to the regulation of quorum sensingin S. typhimurium. The results also show that production of theautoinducer ceases prior to stationary phase in the presence of glucoseat neutral pH and in the absence of glucose at low pH. Therefore, acombination of acidic conditions and the absence of glucose is notrequired to cue S. typhimurium to terminate production of auto inducer.

In addition to glucose, growth on several other carbohydrates alsoinduces production of the signaling activity. These include both PTS(fructose, mannose, glucitol, and glucosamine) and non-PTS (galactoseand arabinose) sugars. These findings eliminate an exclusive role forthe PTS in the regulation of autoinducer biosynthesis. When the S.typhimurium LT2 are grown on several other carbon sources (acetate,glycerol, citrate and serine) no significant accumulation of signalingactivity is observed. We have demonstrated in Example 1 that the signalis not any of a number of substances known to be secreted by S.typhimurium including the major products of mixed acid fermentation.Clearly, production of the signaling compound is precisely regulated bythe cells and is favored under conditions of growth on preferredcarbohydrates for reasons that we do not yet understand. Identificationof the signaling compound and cloning of the biosynthetic gene(s) willaid in a fuller understanding of the regulation process.

Results presented in this example show that, in contrast to other quorumsensing systems, the S. typhimurium signal does not accumulate instationary phase. At least two competing processes contribute to thisregulation; autoinducer production and autoinducer degradation. In thisexample we are defining autoinducer production as an increase in thesignaling activity present in cell-free fluids. We recognize that anincrease in activity could result from release of newly biosynthesizedautoinducer, release of stored autoinducer, repression of degradation ofautoinducer, or some combination of these activities. We defineautoinducer degradation as the disappearance of signaling activity fromthe cell-free fluids. This disappearance could be due to destruction ofthe autoinducer, reuptake of the autoinducer, or a combination of theseactivities. It is possible that under some of the conditions used in ourstudies, autoinducer production and autoinducer degradation areoccurring simultaneously. If this is the case, the activity detected incell-free culture fluids is a measure of which of these processes,production or degradation, predominates. These findings indicate thatquorum sensing in S. typhimurium is regulated such that the signal andpresumably the response to the signal do not persist into stationaryphase. Because the utilization of a preferred carbohydrate is alsorequired for signal production, quorum sensing in S. typhimurium may beused both for measuring the cell density and for measuring the potentialof the environment for growth.

Osmolarity Influences Signal Production and Degradation in S.typhimurium. S. typhimurium cells that are actively producing signal canbe further stimulated to produce signal by specific environmentaltreatments, indicating that several independent regulatory pathwayschannel information into autoinducer synthesis. One of these treatmentsis 0.4 M NaCl osmotic shock. When autoinducer producing S. typhimuriumcells are resuspended in 0.4 M NaCl, the cells release significantlygreater activity when they have the capability to synthesize proteinthan when protein synthesis is blocked. Furthermore, degradation of thesignal also requires protein synthesis. These results have severalimplications. First, in the presence of Cm, S. typhimurium resuspendedat both high and low osmolarity produce a similar amount of activity.This result indicates that, following growth in the presence of glucose,the S. typhimurium cells have a predefined capacity to produce signalingactivity (and/or to release already synthesized activity from the cell).Second, when the cells are resuspended at high osmolarity, signalproduction increases well beyond this level. This increase in signalproduction requires protein synthesis, and we interpret this to meanthat high osmolarity is one environmental cue that induces S.typhimurium to synthesize more of the biosynthetic apparatus necessaryfor signal production and/or release. Third, under conditions of lowosmolarity, we observe an initial release of activity, followed by arapid degradation of the activity. And, signal degradation requiresprotein synthesis because it is not observed in the presence of Cm.These results imply that the environment has changed from conditionsfavoring autoinducer production (LB+ a preferred carbohydrate, or highosmolarity) to conditions where autoinducer production is not favored(low osmolarity, or absence of a preferred carbon source). Thisenvironmental change induces S. typhimurium to synthesize the protein(s)required for degradation of the signaling activity.

When the S. typhimurium cells were incubated in 0.4 M NaCl nosignificant degradation of the activity occurred by 200 min. This resultindicates that either the necessary degradative protein(s) are notsynthesized under these conditions, or alternatively, the degradativeapparatus is assembled, but its activity is inhibited by highosmolarity. The results show that high osmolarity does not inhibitsignal degradation, because cells induced to degrade the activity can doso at high osmolarity. Therefore, the persistence of the activity in thehigh NaCl samples occurs because the degradation machinery is notsynthesized, not because its activity is inhibited.

It is difficult to precisely determine when S. typhimurium cells areautoinducer producers and when they are autoinducer degraders becauseboth processes could occur simultaneously. It appears, however, that noor very low degradation occurs in high osmolarity, and conversion ofcells from overall signal producers to overall signal degraders occursin low osmolarity and requires protein synthesis. Our preliminarycharacterization of the degradative process indicates that it iscell-associated because the autoinducer activity is stable in cell-freeculture supernatants for long periods of time, and combining active withinactive cell-free culture fluids or active and inactive high and lowosmolarity cell-free fluids does not promote degradation of theautoinducer. We have recently isolated a S. typhimurium mutant that doesnot produce the AI-2 activity. If this mutant retains the capability todegrade autoinducer, analysis of it will be informative forunderstanding the timing of degradation, and for identifying the cuesthat induce the degradative machinery. We are currently attempting toisolate S. typhimurium mutants capable of autoinducer production butincapable of autoinducer degradation.

The Role for Quorum Sensing in Salmonella Pathogenesis. The observationspresented here on the regulation of signal production and degradation byS. typhimurium LT2 implicate a role for quorum sensing in pathogenesisof Salmonella. The conditions favoring signal production (nutrient rich,high osmolarity and low pH) are those likely to be encountered upon thefirst interaction of an enteric pathogen with its host. Conditionsfavoring degradation of the signal (nutrient poor, low osmolarity) arethose most probably encountered as the pathogen exits the host. Theinitial colonization of the host may be a concerted effort between apopulation of cells coordinated through this cell-cell signaling system.Other cues, that we have not yet tested, could also regulate quorumsensing in S. typhimurium. These may represent independent oroverlapping signaling pathways involved in pathogenesis. We areisolating S. typhimurium mutants to test these hypotheses. Finally,Salmonella pathogenesis is a dynamic process of interaction between thehost and metabolically active bacteria. Consistent with a role forquorum sensing in pathogenesis, our evidence suggests that this quorumsensing system is not functioning during stationary phase. We have shownthat the signaling compound is not produced during stationary phase, andfurthermore, existing signal is degraded. Perhaps quorum sensing iscritical for S. typhimurium to undergo the transition between ahost-associated and a free-living existence.

EXAMPLE 3 Quorum Sensing in Escherichia coli, Salmonella typhimurium andVibrio harveyi: A New Family of Genes Responsible for AutoinducerProduction

In this example we report the analysis of a gene responsible for AI-2production in V. harveyi, E. coli and S. typhimurium. The geneidentified in all three species of bacteria is highly homologous, and wepropose that these genes define a new family of proteins involved inautoinducer production. The genes, which we named luxS_(V.h.),luxS_(E.c.), and luxS_(S.t.) have been identified in many species ofbacteria by genome sequencing projects, but until now no function hasbeen ascribed to this gene in any organism. The luxS genes do not bearhomology to any other gene known to be involved in autoinducerproduction.

Material and Methods

Bacterial strains, media and recombinant DNA techniques. V. harveyiBB120 is the wild type strain (Bassler et al., 1997, supra). S.typhimurium strain LT2 was obtained from Dr. K. Hughes (University ofWashington), S. typhimurium 14028 is ATCC strain 14028 Organism:Salmonella choleraesuis. E. coli O157:H7 is a clinical isolate suppliedby Dr. Paddy Gibb (University of Calgary). Luria broth (LB) contained 10g Bacto Tryptone (Difco), 5 g Yeast Extract (Difco) and 10 g NaCl perliter. The recipe for Autoinducer Bioassay (AB) medium has been reportedpreviously (Greenberg, E. P., Hastings, J. W., and Ulitzur, S. (1979)Arch. Microbiol. 120, 87-91). Where specified, glucose was added from asterile 20% stock to a final concentration of 0.5%. Antibiotics wereused at the following concentrations (mg/L): Ampicillin (Amp) 100,Chloramphenicol (Cm) 10, Gentamycin (Gn) 100, Kanamycin (Kn) 100, andTetracycline (Tet) 10. DNA isolation, restriction analysis andtransformation of E. coli was performed as described by Sambrook et al.Probes for Southern Blot analysis were labeled using the Multiprime DNAlabeling system of Amersham. Sequencing was carried out using an AppliedBiosystems sequencing apparatus. The V. harveyi BB120 genomic librarywas constructed in the cosmid pLAFR2 as described (Bassler et al., 1993,supra). The method for Tn5 mutagenesis of cloned V. harveyi genes, andthe allelic replacement technique for inserting Tn5 mutated genes intothe V. harveyi chromosome have been reported (Bassler et al., 1993,supra).

Bioluminescence Assay. The AI-2 bioassay using the V. harveyi reporterstrain BB170 (Sensor 1⁻, Sensor 2⁺) has been discussed in the previousexamples. Cell-free culture fluids from V. harveyi, E. coli, or S.typhimurium strains to be tested for AI-2 activity were prepared asdescribed above, and assayed at 10% (v/v). AI-2 activity is reported asthe fold-induction of the reporter strain over background, or as thepercent of the activity obtained from V. harveyi BB120 (wild type)cell-free culture fluid.

Mutagenesis and analysis of the AI-2 production gene in S. typhimuriumLT2. MudJ insertion mutants of S. typhimurium LT2 were generated using aphage P22 delivery system as described (Maloy, S. R., Stewart, V. J.,and Taylor, R. K. (1996) Genetic analysis of pathogenic bacteria: alaboratory manual. Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y.). Following growth to mid-exponential phase in LBcontaining 0.5% glucose, the S. typhimurium insertion mutants weretested for AI-2 production using the V. harveyi BB170 bioassay. The siteof the MudJ insertion that inactivated the AI-2 production function inS. tyhimurium was identified by PCR amplification and sequencing of thechromosomal DNA at the insertion junction. A two-step amplificationprocedure was used (Caetano-Annoles, G. (1993) Meth. Appl. 3, 85-92). Inthe first PCR reaction, the arbitrary primer5′-GGCCACGCGTCGAC-TAGTACNNNNNNNNNNACGCCC-3′ (SEQ ID NO: 21), and theMudJ specific primer 5′-GCACTACAGGCTTGCAAGCCC-3′ (SEQ ID NO: 22) wereused. Next, 1 μl of this PCR reaction was used as the template in asecond PCR amplification employing a second arbitrary primer(5′-GGCCACGCGTCGACTAGTCA-3′)(SEQ ID NO: 23) and another MudJ specificprimer (5′-TCTAATCCATCAGATCCCG-3′) (SEQ ID NO: 24). The PCT product fromthe second reaction was purified and sequenced.

Cloning and sequencing of the E. coli MG1655, E. coli O157:H7, and E.coli DH5 AI-2 production genes. The DNA sequence obtained from the S.typhimurium LT2 MudJ screen was used to search the E. coli MG1655 genomesequence to identify the corresponding E. coli region (Blattner et al.,Science 277, 1453-1462, 1997). The gene identified from the sequencingproject had the designation ygaG. Primers that flanked the ygaG gene andincorporated restriction sites were designed and used to amplify the E.coli MG1655, E. coli 0157:H7 and E. coli DH5 ygaG genes. The primersused are: 5′-GTGAAGCTTGTTTACTGACTAGATC-3′ (SEQ ID NO: 24) and5′-GTGTCTAGAAAAACACGCCTGACAG-3′ (SEQ ID NO: 25). The PCR products werepurified, digested and cloned into pUC19. In each case, the PCR productsfrom three independent reactions were cloned and sequenced.

Results

Identification and cloning of the gene responsible for AI-2 productionin V. harveyi. We have discussed in previous examples that, unlike manyother E. coli strains, E. coli strain DH5 does not produce an AI-2signal compound that can be detected by V. harveyi. We reasonedtherefore, that we could use E. coli DH5 as a mutant to clone the V.harveyi AI-2 production gene. A library of wild type V. harveyi BB120genomic DNA was transformed into E. coli strain DH5, and thetransformants were screened for AI-2 production in the V. harveyi BB170AI-2 detection bioassay. The library consisted of 2,500 clones eachcontaining roughly 25 kb of V. harveyi genomic DNA. Five DH5 clones wereidentified that resulted in upwards of 300-fold stimulation of thereporter strain in the bioassay.

The recombinant cosmid DNA from the five AI-2 producing E. coli DH5clones was analyzed by restriction analysis and Southern blotting. Allfive of the cosmids contained an overlapping subset of identical V.harveyi genomic restriction fragments, indicating that we had cloned thesame locus several times. One cosmid, called pBB2929 was selected forfurther analysis. Random mutagenesis using transposon Tn5 was carriedout on cosmid pBB2929, and pools of cosmids harboring Tn5 insertionswere subsequently transformed into E. coli DH5. We tested 962 individualE. coli DH5/pBB2929::Tn5 strains for the loss of the ability to produceAI-2. Four E. coli DH5 strains harboring Tn5 insertions in pBB2929 wereidentified that failed to produce AI-2. We mapped the locations of theseTn5 insertions in pBB2929 and found that all four transposon insertionsresided in the same 2.6 kb HindIII V. harveyi genomic DNA fragment (FIG.9A).

Cosmid pBB2929 was digested with HindIII and the 8 resulting fragmentswere subcloned in both orientations into pALTER (Promega). The pALTERsubclones were transformed into E. coli DH5, and subsequently tested forAI-2 production. The only strains capable of producing AI-2 containedthe 2.6 kb HindIII fragment identified in the Tn5 mutagenesis. Thisfragment was sequenced, and only one open reading frame (ORF) could beidentified, and its location corresponded to the map positions of thefour Tn5 insertions that eliminated AI-2 production. We named the ORFluxS_(V.h.) (FIG. 9A).

Mutagenesis of luxS_(V.h.) in V. harveyi. We analyzed the effects ofluxS_(V.h.) null mutations on AI-2 production in V. harveyi. The fourTn5 insertions that mapped to the luxS_(V.h.) gene and the control Tn5insertion adjacent to the luxS_(V.h.) locus were transferred to thecorresponding locations in the V. harveyi BB120 chromosome to makestrains MM37, MM30, MM36, MM38 and MM28 respectively (FIG. 9A). Southernblotting was used to confirm the correct placement of all five Tn5insertions in the V. harveyi chromosome. The four V. harveyiluxS_(V.h.)::Tn5 insertion strains were tested for the ability toproduce AI-2, and all four strains gave identical results.

In FIG. 10A, we show the AI-2 production phenotypes of the wild typecontrol Tn5 insertion strain MM28 and one representativeluxS_(V.h.)::Tn5 insertion strain, MM30. V. harveyi MM28 and MM30 weregrown to high cell density, after which cell-free culture fluids wereprepared. The culture fluids were assayed for AI-2 activity by theability to induce luminescence in the AI-2 detector strain BB170. FIG.10A shows that addition of culture fluids from the control Tn5 insertionstrain MM28 induced luminescence in the reporter 780-fold, while culturefluid from the luxS_(V.h.)::Tn5 insertion strain MM30 did not induce theexpression of luminescence in the reporter. Therefore, a null mutationin luxS_(V.h.) in V. harveyi eliminates AI-2 production.

Identification and analysis of S. typhimurium autoinducer productionmutants. In order to identify the gene responsible for AI-2 productionin S. typhimurium, we randomly mutagenized S. typhimurium LT2 using theMudJ transposon (Maloy et al., 1996, supra). Ten-thousand S. typhimuriumLT2 insertion mutants were assayed for AI-2 production in the V. harveyiBB170 bioassay. One S. typhimurium MudJ insertion mutant (strain CS132)was identified that lacked detectable AI-2 in culture fluids atmid-exponential phase.

FIG. 10B shows the AI-2 production phenotypes of S. typhimurium strainLT2 and the corresponding MudJ insertion strain CS132. The strains weregrown to mid-exponential phase in LB containing glucose, and cell-freeculture fluids were prepared and assayed for AI-2. S. typhimurium LT2culture fluids induced the reporter strain 500-fold, while culturefluids from strain CS132 contained no AI-2 activity. Furthermore, strainCS132 did not produce AI-2 under any of the growth conditions that wehave previously reported induce AI-2 production in S. typhimurium (notshown).

The site of the MudJ insertion in S. typhimurium CS132 was determined byPCR amplification followed by sequencing of the 110 bp of chromosomalDNA adjacent to the transposon. This sequence was used to search thedatabase for DNA homologies. The sequence matched a site (89/105 bpidentity) in the E. coli MG1655 genome that corresponded to an ORF ofunknown function denoted ygaG (Blattner et al., 1997, supra). In thechromosome, the E. coli ygaG gene is flanked by the gshA and emrB genes(FIG. 9B). The ygaG gene is transcribed from its own promoter that islocated immediately upstream of the gene, indicating that it is not inan operon with gshA. The emrB gene is transcribed in the oppositedirection. We PCR amplified the ygaG region from the chromosomes of E.coli O157:H7 and E. coli MG1655, and the two E. coli ygaG genes werecloned into pUC19.

Complementation of S. typhimurium and E. coli AI-2⁻ mutants. We testedwhether the E. coli O157:H7 ygaG gene and the V. harveyi luxS_(V.h.)gene could restore AI-2 production in the AI-2⁻ strains S. typhimuriumCS132 and E. coli DH5. In FIG. 11A, we show the AI-2 activity producedby wild type V. harveyi BB120, E. coli O157:H7 and S. typhimurium LT2.In this figure, the level of AI-2 activity present in V. harveyi BB120cell-free culture fluids was normalized to 100%, and the activities incell-free culture fluids from E. coli and S. typhimurium compared tothat. In this experiment, E. coli O157:H7 produced 1.5 times and S.typhimurium LT2 produced 1.4 times more AI-2 activity than V. harveyiBB120 (i.e., 150% and 141% respectively).

FIGS. 12A and 12B show the AI-2 complementation results for S.typhimurium CS132 and E. coil DH5. FIG. 12A demonstrates thatintroduction of the E. coli O157:H7 ygaG gene into S. typhimurium CS132restored AI-2 production beyond the level of production of wild type S.typhimurium (i.e., 209% activity). Comparison of the data in FIG. 12Aand 12B shows that the E. coli ygaG gene in S. typhimurium resulted inAI-2 production exceeding that produced in vivo by E. coli O157:H7.Introduction of the V. harveyi luxS_(V.h.) gene into S. typhimuriumresulted in AI-2 production at slightly less than the level produced bywild type V. harveyi BB120 (i.e., 73% of the level of V. harveyi BB120).FIG. 12B shows that E. coli DH5 was also complemented to AI-2 productionby both the cloned E. coli O157:H7 and the V. harveyi BB120 AI-2production genes. However, introduction of E. coli O157:H7 ygaG and V.harveyi BB120 luxS_(V.h.) into E. coli DH5 resulted in only 31% and 43%of the V. harveyi BB120 AI-2 activity respectively. FIG. 12A and 12Bshow that the control vectors produced no activity in thecomplementation experiments.

Analysis of the AI-2 production genes from V. harveyi, E. coli and S.typhimurium. We sequenced the AI-2 production gene luxS_(V.h.) from V.harveyi BB120 and the ygaG loci from E. coli O157:H7, E. coli MG1655 andE. coli DH5. The translated protein sequences encoded by the ygaG ORF'sare shown in FIG. 13, and they are aligned with the translated LuxSprotein sequence from V. harveyi. The nonbold, underlined amino acidsindicate the residues in the E. coli proteins that differ from the V.harveyi LuxS protein. The ygaG loci from E. coli encode proteins thatare highly homologous to one another and also to LuxS from V. harveyi.The E. coli MG1655 and the E. coli O157:H7 YgaG proteins are 77% and 76%identical to LuxS from V. harveyi BB120. The DNA sequence we determinedfor ygaG from E. coli O157:H7 differs at five sites from the reported(and our) sequence for the E. coli MG1655 ygaG gene. Four of the changesare silent, the fifth results in a conservative Ala to Val alteration atamino acid residue 103 in the E. coli O157:H7 protein.

Identification of the ygaG locus in E. coli MG1655 and E. coli O157:H7allowed us to investigate the AI-2 production defect in E. coli DH5. E.coli DH5 possesses the ygaG gene because we could PCR amplify thisregion from the chromosome using the same primers we employed to amplifyit from E. coli MG1655 and E. coli O157:H7. Examination of the E. coliDH5 ygaG promoter showed that it is identical to that of E. coli MG1655,indicating that the AI-2 defect in E. coli DH5 is not simply due todecreased transcription of ygaG. However, sequence analysis of the E.coli DH5 ygaG coding region showed that a one G-C base pair deletion anda T to A transversion exist at bp 222 and 224 respectively. Theframeshift mutation resulting from the G/C deletion causes prematuretruncation of the E. coli DH5 protein. FIG. 13 shows that the truncatedE. coli DH5 protein is 111 amino acids, while the E. coli MG1655 and E.coli O157:H7 proteins are 171 residues. Twenty altered amino acids aretranslated after the frame shift and prior to termination of theprotein. Our complementation results (FIGS. 11 and 12) demonstrate thatthe AI-2 production defect in E. coli DH5 is recessive to in transexpression of ygaG, which is consistent with the defect being due to anull mutation caused by the frame shift in the E. coli DH5 ygaG gene.

We searched the S. typhimurium database using the sequence we obtainedadjacent to the MudJ that inactivated the AI-2 production function in S.typhimurium CS132. A perfect match (110/110 bp) was identified tofragment B_TR7095.85-T7 in the S. typhimurium LT2 genome sequencingdatabase (Genome Sequencing Center, Washington University, St. Louis).However, the S. typhimurium LT2 database ygaG sequence is incomplete(FIG. 13). The translated sequence matches the E. coli and V. harveyisequences beginning at amino acid residue 8. The translated sequenceshows that the S. typhimurium protein is 75% identical to LuxS of V.harveyi. In order to align the S. typhimurium sequence with the V.harveyi LuxS protein, we corrected three apparent frame shift errors inthe database sequence. Considering that only crude, unannotated sequencedata is currently available for S. typhimurium, we predict that the S.typhimurium protein contains 7 more amino acids, and that the frameshift mutations are sequencing errors. We were unsuccessful at PCRamplifying either the S. typhimurium 14028 or the S. typhimurium LT2ygaG gene using the primers designed for E. coli, so we do not yet havethe complete sequence of the S. typhimurium gene.

The results set forth above indicate that the genes we have identifiedand analyzed encode a novel family of proteins responsible forautoinducer production. Members of this new family of genes, referred toherein as LuxS, are highly homologous to one another but not to anyother identified genes. The encoded product of the LuxS genes catalyzean essential step in the synthesis of the signaling compounds of thepresent invention.

EXAMPLE 4 Construction of a Sensor 1⁻, AI-2⁻ V. harveyi Reporter Strain

V. harveyi null mutants in each of the lux genes luxL, luxM, luxN, luxSand luxQ have been constructed. These mutants fail to either make orrespond to one specific autoinducer, but they still produce lightbecause, in each case, one quorum sensing system remains operational. Adouble luxN, luxS V. harveyi mutant will not emit light without theaddition of exogenous AI-2 because this mutant will not respond to AI-1and it will not produce AI-2.

The V. harveyi luxS gene has been cloned into E. coli DH5a on a broadhost range mobilizable cosmid called pLAFR2. This construction restoresAI-2 production to E. coli DH5α. A marked null mutation was engineeredinto the luxS gene by introducing a chloramphenicol resistance (Cm^(r))cassette into an internal restriction site. Placement of the Cm^(r)cassette at this site in luxS subsequently eliminated AI-2 production inE. coli DH5α.

The luxS::Cm^(r) null allele was transferred onto the chromosome of V.harveyi strain BB170. Strain BB170 contains a Tn5Kanr in luxN and doesnot respond to AI-1. To construct the double mutant, triparentalconjugations were carried out by mixing stationary phase cultures of E.coli DH5α carrying the V. harveyi luxS::Cm^(r) construction in pLAFR2(pLAFR2 carries tetracycline resistance), E. coli DH5α carrying the tradonor plasmid pRK2013 and the V. harveyi recipient strain BB170.Exchange of the luxS::Cm^(r) mutant allele for the wild type luxS alleleon the chromosome occurs by homologous recombination. The exogenotecosmid in V. harveyi was eliminated by the introduction of a secondincompatible plasmid pPH1JI. This was accomplished by mating E. coliDH5α containing pPH1JI with the V. harveyi BB170 recipient containingthe luxS::Cm^(r) cosmid, and selecting for exconjugants on platescontaining ampicillin (for counter selection of the E. coli donor)chloramphenicol (for inheritance of the mutant luxS::Cm^(r) allele) andgentamicin (for maintenance of the plasmid pPH1JI). Southern blotanalysis was used to verify that the exogenote pLAFR2 cosmid has beeneliminated and that the luxS::Cm^(r) construction had been transferredto the corresponding position in the genome of V. harveyi. The pPH1JIcosmid was subsequently eliminated by growth in the absence ofgentamicin selection.

Verification that the luxN, luxS Double Mutant Responds to AI-2. The Vharveyi strain that is mutant in luxN and luxS was stimulated to producelight in response to the exogenous addition of AI-2 but not AI-1. Thiswas verified in a luminescence assay for response to V. harveyi AI-1 andAI-2. V. harveyi strain MM30 (luxS::Tn5) that is phenotypically AI-1⁺,AI-2⁻, and V. harveyi strain BB152 (luxM::Tn5) that is phenotypicallyAI-1⁻, AI-2⁺ were used as the sources of AI-1 and AI-2 respectively. TheAI-1 and AI-2 present in culture fluids of these strains was tested forstimulation of light production of the V. harveyi luxN, luxS doublemutant reporter strain. In this assay, autoinducer preparations fromMM30, BB152 or sterile medium controls were added to the wells ofmicrotiter plates, followed by the addition of the V. harveyi reporterstrain. The resulting light production was monitored using a liquidscintillation counter in the chemiluminescence mode. Maximal stimulationof light production in the V. harveyi luxN, luxS reporter strain wascompared to that produced by the Sensor 1⁺, Sensor 2⁻ V. harveyi strainBB886 and the Sensor 1⁻, Sensor 2⁺ V. harveyi strain BB170. These two V.harveyi strains are routinely used in this assay as reporters of AI-1and AI-2 activity respectively.

Determine optimum concentrations of AI-2 in microtiter assays. Theaformentioned screen will be optimized for use in 96-well microtiterassays. The screen will be used in inhibitor assays for identifyinginhibitors of AI-2. Purified or synthetic AI-2 will be added to themicrotiter wells containing the newly constructed reporter strain andinhibition will be measured by a decrease in light emission from thewells containing an inhibitor. The assay will be optimized bydetermining the concentration of cells and AI-2 in the microtiter wellsthat will allow for maximal sensitivity. The optimal AI-2 concentrationwill be that that stimulates half-maximal light output for a givenconcentration of cells per unit time. Initial experiments will beconducted in this concentration range to determine the range of AI-2concentration that produces the greatest change in light output. Similarexperiments using AI-1 and a non self-stimulating sensor-1⁺, sensor-2⁻mutant (BB886) showed that the assay was sensitive to concentrations aslow as 100 nM AI-1 and that light emission was linear over 6 orders ofmagnitude (light emission from a self-stimulating strain was linear over3 orders). Similar results for AI-2 using the new reporter strain thatwill not self-stimulate and therefore have zero background lightemission are predicted. Light emission from the microtiter wells will bemeasured with a Wallac TriLux liquid scintillation counter model1450-021 in the chemiluminescence mode. This machine will accommodate 16plates and will therefore allow for 1536 separate concentrationexperiments per run.

EXAMPLE 5 In-Vitro Method for Synthesizing AI-2

Purification and Identification of AI-2. The AI-2 class of compound isrefractory to purification by conventional techniques used for theisolation of acyl-homoserine lactone (HSL) autoinducers such as AI-1from V. harveyi. Unlike other HSL autoinducers, under the conditionstested, the AI-2 activity does not extract quantitatively into organicsolvents. Furthermore, it fails to bind to either a cation or anionexchange column. The present characterization of AI-2 indicates that ithas a molecular weight of less than 1000 kDa, and is a polar butapparently uncharged organic compound. The AI-2 activity is acid stableand base labile and heat resistant to about 80 but not 100° C. Theseresults indicate that the AI-2's are not acyl-homoserine lactones. TheluxS genes identified in the present study bear no homology to othergenes known to be involved in production of HSL autoinducers furtherindicating that the present AI-2 class of autoinducers is novel.

Thus, in addition to providing a cloned, overexpressed and purified S.typhimurium LuxS protein, the present invention also provides a methodfor producing AI-2 in vitro. The present invention provides a mechanismfor generating large quantities of pure AI-2 useful for mass spectraland NMR analysis, and for screening compounds that modulate the activityof AI-2. Moreover, the present invention provides a method fordetermining the in vivo biosynthetic pathway for AI-2 synthesis.

The analysis of the genomic locations of the various luxS genesidentified in the present invention indicates that the luxS genes do notconsistently reside in any one location in the chromosome, nor are theytypically found in close proximity to any specific gene(s). However, inone case, the luxS gene is the third gene in a three-gene operon withtwo genes (metK and pfs). In E. coli, Salmonella and many otherbacteria, MetK and Pfs are involved in the conversion of S-adenosylmethionine (SAM) to homocysteine and 4,5-dihydroxy-2,3 pentanedione(FIG. 14). The function of MetK is to convert methionine to SAM that isan important cofactor in one-carbon metabolism. SAM is used to methylateDNA, RNA and a variety of cell proteins, and several SAM dependentmethyl transferases act at this step. S-adenosyl homocysteine (SAH) isproduced when the methyl group is transferred from SAM to itssubstrates. SAH functions as a potent inhibitor of SAM dependentmethyltransferases. Therefore, bacteria rapidly degrade SAH via theenzyme Pfs. The designation “pfs” refers to an open reading frame in theE. coli genome that has recently been determined to encode the enzyme5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase, also knownas MTA/SAH nucleosidase. In the present system, the enzyme cleaves theglycosidic bond in S-adenosylhomocycteine (SAH). Thus, the function ofPfs is to convert SAH to adenine and S-ribosyl homocysteine. In a finalstep, S-ribosyl homocysteine is converted to homocysteine and4,5-dihydroxy-2,3-pentanedione. Homocysteine can reenter this pathway;it is methylated to generate methionine that can be converted to SAM byMetK.

The catabolism of SAH is considered a salvage pathway for recyclingmetabolic intermediates (adenine and homocysteine). However, somespecies of bacteria eliminate SAH by a different pathway. In thisalternative pathway, adenosine is directly removed from SAH thatgenerates homocysteine. Therefore, cells that use this second mechanismdo not produce 4,5-dihydroxy-2,3-pentanedione. In the pathway shown inFIG. 16, the enzyme responsible for conversion of S-ribosyl homocysteineto 4,5-dihydroxy-2,3-pentanedione has never been identified, cloned orpurified. Furthermore, no role for 4,5-dihydroxy-2,3-pentanedione isknown.

LuxS is involved in the pathway shown in FIG. 16, and SAM and SAH areinvolved in AI-2 production. The structure of AI-2 could be4,5-dihydroxy-2,3-pentanedione, in which case LuxS is theuncharacterized enzyme that acts on S-ribosyl homocysteine. Second, LuxScould act on one of the intermediates to make AI-2. LuxS would representa branch point off the known pathway.

To confirm that LuxS is involved in the conversion of SAM to AI-2, thegene encoding the S. typhimurium LuxS protein was cloned, overexpressedand the S. typhimurium LuxS protein was purified. This protein was usedin combination with dialyzed cell-free extracts prepared from a S.typhimurium luxS null mutant to show that addition of SAM and LuxSprotein could restore AI-2 production to dialyzed LuxS- cell extracts.Reaction mixtures were prepared containing 10 mM Sodium Phosphate bufferpH 7.0, dialyzed S. typhimurium LuxS-cell extract and SAM. Purified LuxSprotein was added to some of these mixtures. The reactions wereincubated at room temperature for 60 min, followed by centrifugation ina 5000 MWCO centricon. The material with MW<5000 was added to thestandard V. harveyi bioassay as previously described. Dialyzed LuxS-cellextracts to which SAM was added or extracts containing LuxS proteinwithout the addition of SAM produced no AI-2 activity. However,identical extracts to which LuxS protein and SAM had been added producedAI-2 that resulted in over 500-fold stimulation in light production inthe bioassay.

Further investigation showed that SAM is not the direct substrate forLuxS, and that LuxS must act at a step subsequent to the conversion ofSAM to SAH (FIG. 16). It was determined that AI-2 was not produced ifSAM was added directly to LuxS protein, however activity was produced bypre-incubation of SAM with the LuxS- extracts, filtration, andsubsequent addition of LuxS protein to the filtrate. Importantly, thesestudies indicate that SAM can react with an element in the cell extractbefore it can be used by LuxS to make AI-2. Presumably, the SAMdependent methyl transferases present in the cell extract use SAM as amethyl donor and convert it to SAH in the process. To verify this, SAHwas substituted for SAM in an in vitro assay. Addition of SAH to the invitro assay resulted in much greater AI-2 production than when SAM wasadded. This result indicates that LuxS functions in the pathwaysubsequent to the conversion of SAM to SAH. Again, addition of SAHdirectly to LuxS protein is not sufficient for production of AI-2activity, while pre-incubation of SAH with dialyzed LuxS- extractsfollowed by filtration and subsequent addition of LuxS protein to thefiltrates does result in AI-2 production. Presumably SAH is converted toS-ribosyl homocysteine and then LuxS acts to produce AI-2.

The proposed pathway shown in FIG. 16 is not a salvage pathway forrecycling secondary metabolites, but rather is the pathway forproduction of AI-2. The present invention has narrowed the possibilitiesfor point of LuxS activity in the biosynthesis of AI-2. The remainingpossibilities are shown in FIG. 16 (designated LuxS?).

According to the invention, AI-2 is a derivative of ribose. It isnoteworthy that, in V. harveyi, LuxP, the primary sensor for AI-2, is ahomologue of the E. coli and S. typhimurium ribose binding protein.

Characterization and Biosynthesis of AI-2. The invention furtherprovides a method for an in vitro procedure for large scale productionof pure AI-2. As indicated in FIG. 16, SAH is a precursor in the LuxSdependent biosynthesis of AI-2. Furthermore, LuxS does not act directlyon SAH. Prior to the action of LuxS, SAH must first be acted on by someenzyme in dialyzed cell extracts. Presumably this step is the conversionof SAH to S-ribosyl homocysteine by Pfs. Therefore the substrate forLuxS is S-ribosyl homocysteine.

To confirm that LuxS acts on S-ribosyl homocysteine, the Pfs enzyme canbe purified and used to convert SAH to S-ribosyl homocysteine. Towardthis end, the pfs gene has been cloned from S. typhimurium 14028 placedinto the overexpression vector pLM-1. The Pfs enzyme will beoverexpressed and SAH will be added to purified Pfs to produce S-ribosylhomocysteine. The conversion of SAH to S-ribosyl homocysteine will beconfirmed by reverse phase HPLC analysis (SAH is UV active whileS-ribosyl homocysteine is not). Subsequently, the S-ribosyl homocysteineproduced by Pfs will be added to purified LuxS. Following incubation,the mixture will be filtered over a 5000 MWCO centricon. The filtratewill be tested for AI-2 activity in the previously described V. harveyibioassay. The identification of activity will confirm that4,5-dihydroxy-2,3-pentanedione is AI-2.

In addition, AI-2 structure obtained from E. coli and V. harveyi AI-2will be determined. The E. coli and V. harveyi luxS genes have beencloned in to overexpression vectors. The identity/biosynthesis of the S.typhimurium AI-2 provided by the present invention should greatlyfacilitate these analyses. In the event that the S. typhimurium, E. coliand V. harveyi AI-2's are identical these data will indicate that AI-2'sare the same.

EXAMPLE 6 Identification of Compounds that Modulate the Response to AI-2

A library of chemical compounds generated by combinatorial chemistrytechniques is obtained. A plurality of test mixtures is generatedwherein each test mixture contains one or more of the compounds from thelibrary and AI-2. Each of the test mixtures is placed in contact with aculture of Vibrio harveyi MM32 cells and bioluminesce is measured asdescribed above. The amount of bioluminescence from each the culturescontacted with the test mixtures is compared to the amount ofbioluminescence from a control culture of Vibrio harveyi MM32 cells thatwas contacted with AI-2 but not with a compound from the library.

A test mixture that resulted in a reduced level of bioluminescencerelative to the control culture is identified. This test mixturecontains a compound that decreases the response to AI-2. The compound ispurified and its structure is determined. The compound may be directlyuseful as an antimicrobial compound to reduce the extent of an infectionor, alternatively, the compound may be further optimized to produce acompound that may be used to to reduce the extent of an infection.

EXAMPLE 7 Bacterial Strains and Media used to Discover the lsr Operon

The bacterial strains and plasmids used to discover the lsr operon arelisted in Table 4 below. TABLE 4 S. typhimurium Strains and PlasmidsGenotype Source Strain S. typhimurium Strains 14028 Wild type ATCC SS007luxS::T-POP (Schauder et al., 2001) MET89 pqiA::T-POP This study JS14lsrA::MudJ This study JS15 lsrA::MudJ luxS::T-POP This study MET442 JS15with pUC18 This study MET444 JS15 with pAB15 This study MET235lsrC::MudJ This study MET236 lsrC::MudJ luxS::T-POP This study MET281MET236 with pUC18 This study MET276 MET236 with pAB15 This study MET259lsrB::MudJ This study MET260 lsrB::MudJ luxS::T-POP This study MET285MET260 with pUC18 This study MET280 MET260 with pAB15 This study MET233lsrF::MudJ This study MET234 lsrF::MudJ luxS::T-POP This study MET231lsrF::MudJ This study MET239 lsrF::MudJ This study MET240 lsrF::MudJluxS::T-POP This study MET283 MET239 with pUC18 This study MET278 MET239with pAB15 This study MET237 lsrE::MudJ This study MET238 lsrE::MudJluxS::T-POP This study MET282 MET238 with pUC18 This study MET277 MET238with pAB15 This study MET328 rpsL null This study MET341 MET328 ΔlsrRThis study MET342 MET328 ΔlsrR luxS::T-POP This study MET371 lsrC::MudJΔlsrR luxS::T-POP This study MET370 lsrC::MudJ ΔlsrR This study MET450MET236 with pMET1035 This study MET449 MET235 with pMET1035 This studyMET492 MET371 with pMET1035 This study MET453 MET370 with pMET1035 Thisstudy MET269 luxS::pKAS32 This study MET270 lsrC::MudJ luxS::pKAS32 Thisstudy MET301 lsrC::MudJ luxS::pKAS32 lsrRA21T This study undefined T-POPinsertion MET294 lsrC::MudJ luxS::pKAS32 lsrRA120T This study undefinedT-POP insertion MET293 lsrC::MudJ luxS::pKAS32 lsrRG208R This studyundefined T-POP insertion MET299 lsrC::MudJ luxS::pKAS32Δ(P_(lsr)-5′lsrR) This study undefined T-POP insertion MET305 lsrC::MudJluxS::pKAS32 lsrRL145Q This study undefined T-POP insertion MET303lsrC::MudJ luxS::pKAS32 lsrRL134P This study MET309 lsrC::MudJluxS::pKAS32 lsrRL39P This study MET312 lsrC::MudJ luxS::pKAS32 lsrRY25HThis study MET378 lsrC::MudJ luxS::pKAS32 lsrR::T-POP This study JS128metE551 metA22 ilv452 trpB2 hisC527(am) galE496 xyl-404 Slauch, J.rpsL120 flaA66 hsdL6 hsdA29 zjg8103::pir Plasmids pUC18 Amp^(R)(Sambrook et al., 1989) pAB15 pUC18 (Amp^(R)) containing luxS This studypJAF329 pALTER-1 Tet^(S), Amp^(R) This study pMET1035 pJAF329 (Amp^(R))with lsrR This study pKAS32 Amp^(R), rpsL⁺ Suicide vector (Skorupski andTaylor, 1996) pNK2880 Amp^(R), P_(tac)-tnpA (Bender and Kleckner, 1992)

S. typhimurium 14028 is ATCC strain 14028, Organism: Salmonellacholeraesuis. All strains were grown in Luria Broth (LB), whichcontained 10 g Bacto Tryptone (Difco), 5 g Yeast Extract (Difco), and 10g NaCl per liter (Sambrook et al., 1989). When necessary, media weresupplemented by antibiotics at the following concentrations (mg/liter):ampicillin (Amp), 100; kanamycin (Kan), 100; tetracycline (Tet), 10 or15; and streptomycin (Sm), 1000.5-Bromo-4-Chloro-3-indoylyl-β-D-galactoside (X-gal) was added to LB agarplates to a final concentration of 40 mg/liter. MacConkey-lactose andM63-lactose minimal plates were prepared as described (Miller, 1992). ABmedium was prepared as described (Greenberg et al., 1979). All E. coliand S. typhimurium strains were grown at 37□ C with aeration.

EXAMPLE 8 Genetic and Molecular Techniques used in the Discovery of thelsr Operon

DNA ligation reactions were transformed into either E. coli strain JM109(supE Δ(lac-proAB) hsdR17 recAI F⁻ traD36 proAB⁺ lacl^(q) lacZΔM15) orMC4100 λpir (F⁻ araD139 Δ(argF-lac)U169 rpsL150 relA1 thi fib5301 deoC1ptsF25 rbsR λpir) by electroporation. Electroporation of plasmids intobacterial cells was carried out as previously described (Sambrook etal., 1989). Plasmids were maintained in E. coli strains, and passagedthrough the restriction deficient strain S. typhimurium JS128 beforeintroduction into other S. typhimurium strains. P22 transductions wereperformed using P22HT int, as described (Davis et al., 1980). Sequencingreactions were performed by the Princeton University SynSeq facility.Polymerase chain reaction (PCR) reactions were performed using Taq DNAPolymerase (Boeringer Mannheim Biochemicals) or Ex-Taq DNA Polymerase(Takara Biochemicals). Restriction endonucleases and T4 DNA ligase werepurchased from New England Biolabs. All enzymes were used as recommendedby the suppliers. Primers used in PCR and sequencing reactions arelisted in Table 5 below TABLE 5 PCR and Sequencing Primers Primer NameOligonucleotide St-11 ATAAGAATGCGGCCGCAGAGGCGTTAAATGACTGCAACGC St-12GCGGAGCTCTATCGCTCATTGTCATAACCTGGC St-13GCGGAGCTCACTATATCAATGCACTGGTTACCG St-14GCGGAATTCAACAGACTACGTTTCCAGTTGCGG St-15GCGGAATTCTGAAAAAGAAATTGTTCAAAACGG Pop1 CCAAATGATGTTATTCCGCG luxS01CGGGGATCCTTACCGTAATCTGTTACGCG luxS04 GGGGATCCGAAAAGCAAGCACCGATCATC St-18GCGAAGCTTAGCCAGGTTATGACAATGAGCG St-16 GCGGGATCCTAATTTGAATTATTTTCCCTGCGGSt-9 AATAAGTATGCGGCCGCCATTCCGAACAAAGAAGTGATG St-10GGGGAATTCCGCTGCTCGTCCGGCGTGCCAATC

EXAMPLE 9 Identification of AI-2 Regulated Genes in S. typhimurium

The following strategy allowed us to generate 11,000 isogenic wild typeluxS and luxS null strains harboring random MudJ (lacZ) reporterinsertions in the S. typhimurium chromosome. Wild type S. typhimurium14028 was mutagenized with the transposon MudJ by a P22 delivery system,as described (Hughes and Roth, 1988). 11,000 insertion mutants wereordered onto grids on LB plates that contained Kan to select for MudJand 5 mM EGTA to inhibit phage adsorption. In order to create theisogenic wild type luxS and luxS null pairs of mutants for each MudJinsertion, the mutants were replica plated onto two different petriplates. One plate contained a P22 lysate that had been propagated on theluxS null strain SS007 (14028 luxS::T-POP) (Schauder et al., 2001). Thesecond plate contained a P22 lysate that was harvested from wild typeluxS strain MET89 (14028 pqiA::T-POP). The pqiA gene is expected to haveno effect on AI-2 signalling, and thus serves as control for the P22transduction procedure (Koh and Roe, 1995). Both lysates were used at aconcentration of 2%. In addition, all petri plates contained Tet, Kan,X-gal, and 5mM CaC12. Tet was included in the plates to select for T-POPtransductants. Kan was added to ensure that all colonies retained a MudJinsertion. Addition of CaC12 allowed the cells to be infected with P22on the petri plates. X-gal was used as a visual monitor for LacZactivity from the MudJ reporter. The insertion mutants were compared toidentify those with differential β-galactosidase activity in the wildtype luxS and luxS null backgrounds. Colonies containing potential luxSregulated fusions were purified and tested in quantitativeβ-galactosidase assays. Fusions that showed differential β-galactosidaseactivity were backcrossed by P22 transduction into wild type strain14028 and luxS null strain SS007, and subsequently re-examined fordifferential LacZ activity using β-galactosidase assays. In strains thatmaintained differential β-galactosidase activity, the chromosome-MudJtransposon fusion junction was amplified by a two-step PCR method. Thefusion junction was sequenced in order to identify the regulated gene,as described (Surette et al., 1999).

EXAMPLE 10 Isolation of Suppressors of lsr Operon Expression

Strain MET270 (luxS::pKAS32, lsrC::MudJ) is Lac−, and is thereforeunable to grow on M63-lactose minimal plates. To identify mutations inregulators of the lsr operon, a genetic. selection was performed forspontaneous mutations in MET270 that resulted in a Lac⁺ phenotype,indicating that the lsrC::MudJ reporter was transcribed in the absenceof a functional luxS gene. Mutants were selected by plating aliquots(0.1 ml) of overnight cultures of MET270 onto M63-lactose platescontaining Amp and Kan, and incubating at 37□ C. Amp and Kan wereincluded on the plates to ensure that colonies retained theirluxS::pKAS32 and lsrC::MudJ markers, respectively.

In an analogous strategy, transposon T-POP mutagenesis was used toidentify mutants in which the lsr operon was expressed in a luxS nullbackground. A library of 12,000 random T-POP insertions was generated inan S. typhimurium strain containing the lsrC::MudJ fusion and the Tn10transposase expressing plasmid pNK2880, as described (Rappleye and Roth,1997). A P22 lysate was generated on this library of T-POP insertionmutants to transduce the T-POP insertions into MET270. Transductantswere plated on M63-lactose minimal plates containing Amp, Kan, and Tet.Amp and Kan were included to ensure retention of the luxS::pKAS32 andlsrC::MudJ markers, respectively. Tet was included to select for T-POPtransductants. To verify that the suppressor mutations were associatedwith the T-POP insertions, linkage of the suppressor mutations to theT-POP insertions was determined by transduction. The T-POP marker wastransduced into MET270 and plated on MacConkey-lactose plates containingAmp, Kan, and Tet, to select for the luxS::pKAS32, lsrC::MudJ, and T-POPmarkers, respectively. A Lac⁺ phenotype was taken as evidence that thesuppressor mutation was associated with the T-POP insertion.

To determine whether the suppressor mutations were linked to the lsroperon, the lsrC::MudJ marker from each mutant was transduced intostrain MET269 (luxS::Pkas32) and plated on MacConkey-lactose platescontaining Kan and Amp. Amp was included in these plates to maintain theluxS::Pkas32 construct, and Kan was included to select for MudJ.Co-transduction of the suppressor mutation with the lsrC::MudJ fusionwas assessed by scoring the presence of Lac⁺ colonies, which indicatedthat the suppressor mutation was linked to the lsr operon. To determinewhether the T-POP transposon had inserted in lsrR, the lsrR gene was PCRamplified from the suppressor strains using primers St-11 and St-14.Suppressors generating no PCR product from this reaction were inferredto have a T-POP insertion in the lsrR gene. The T-POP-lsrR fusionjunction was PCR amplified from these strains using T-POP primer Popland lsrR primers St-14 and St-15. The products were sequenced to definethe positions of the T-POP insertions in lsrR. The lsrR gene of thespontaneous Lac⁺ suppressors was PCR amplified and sequenced to identifythe mutations.

EXAMPLE 11 Plasmid Constructions

To construct plasmid pAB15, the S. typhimurium luxS gene and flankingsequences were amplified from the chromosome of S. typhimurium 14028 bypolymerase chain reaction (PCR), using primers luxS01 and luxS04. Theseprimers introduce BamHI restriction sites. The resulting PCR product wasdigested with BamHI and ligated into BamHI-digested pUC18. To constructplasmid pMET1035, the lsrR gene was amplified by PCR from the chromosomeof S. typhimurium 14028 using primers St-18 and St-16, which introduceHindIII and BamHI restriction sites, respectively. The parent vector forthis cloning procedure, pJAF329, was created by site-directedmutagenesis of plasmid pALTER-1 (Promega) to create an AmpR, Tetsversion of the vector. The lsrR PCR product was digested with HindIIIand BamHI and ligated into similarly digested pJAF329. Transcription ofthe lsrR gene in this construct is driven from a constitutive promoterin pJAF329.

EXAMPLE 12 Construction of the luxS::pKAS32 Null Strain

A 200 bp DNA fragment internal to luxS was amplified by PCR from thechromosome of S. typhimurium 14028 using primers St-9 and St-10 (Table2). The PCR product was digested with NotI and EcoRI and ligated intothe suicide plasmid pKAS32 (Skorupski and Taylor, 1996). The resultingluxS suicide plasmid was transformed into S. typhimurium 14028.Selection on LB plates containing Amp induced the plasmid to integrateinto the chromosome at the luxS locus. Inactivation of luxS was verifiedby demonstrating that this strain produced no AI-2 in our AI-2 bioassay(Bassler et al., 1997). This strain is called MET269.

EXAMPLE 13 Construction of an Inframe lsrR Deletion

The DNA flanking the 5′ region of lsrR was PCR amplified from S.typhimurium 14028 using primers St-11 and St-12. Similarly, the 3′flanking region was amplified with primers St-13 and St-14. The 5′sequence was digested with NotI and SacI, and the 3′ sequence with SacIand EcoRI. The suicide plasmid Pkas32 was digested with NotI and EcoRI.A three-part ligation was performed in order to clone the lsrR flankingregions into Pkas32. This lsrR deletion construct was transformed intoE. coli strain MC4100 □pir by electroporation. The lsrR deletion wassubsequently transferred to the chromosome of S. typhimurium strainMET328 by the two step suicide delivery system of Skorupski and Taylor(Skorupski and Taylor, 1996).

EXAMPLE 14 AI-2 Activity Assay

Relative levels of AI-2 in cell-free culture fluids of S. typhimuriumstrains of interest were measured using a V. harveyi bioluminescenceassay, as described previously (Bassler et al., 1993; Bassler et al.,1997). Cell-free culture fluids were prepared as described (Surette andBassler, 1998; Surette et al., 1999). These preparations were assayedfor AI-2 activity at 10% (vol/vol), using V. harveyi reporter strainBB170 (luxN::Tn5), as described (Bassler et al., 1993). AI-2 activity isreported as fold induction over background of bioluminescence. Toexamine the role of Lsr in the uptake of AI-2, cultures of S.typhimurium were grown overnight, diluted 1:100 into fresh LB, and grownfor a total of 4 hours. During the final hour of growth, the cells wereincubated with 70 μM in vitro prepared AI-2 for specified times(Schauder et al., 2001). Subsequently, the cultures were chilled on iceand cell-free culture fluids were prepared. The AI-2 remaining in thesepreparations was measured in the V. harveyi bioluminescence assay.Assays were performed in duplicate.

EXAMPLE 15 β-galactosidase Assays

Cultures of S. typhimurium that had been grown overnight were diluted1:100 into fresh LB and grown for 4 hours. For strains containingplasmids, cultures were diluted in LB supplemented with Amp. Whennecessary, AI-2 was synthesized in vitro and added to the growth mediaat the time of inoculation (Schauder et al., 2001). Cells from 1 ml ofthese cultures were harvested and resuspended in 1 ml Z buffer.β-galactosidase assays were performed using a microtitre plate assay, asdescribed (Slauch and Silhavy, 1991). β-galactosidase units werecalculated as (0.1*mOD420/min)/[OD₆₀₀ of cells*Volume (ml)]. All assayswere performed in triplicate.

The present invention is not limited to the embodiments described andexemplified above, but is capable of variation and modification withinthe scope of the appended claims.

The following references are incorporate by reference herein in theirentireties:

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 26. (canceled)
 27. (canceled)
 28. A method foridentifying a compound that modulates the response to a firstautoinducer that is not an acyl-homoserine lactone and that can interactwith the Vibrio harveyi LuxQ protein, thereby inducing expression of aVibrio harveyi operon comprising the luxCDABE genes, comprising:obtaining a cell having increased expression of a transporter thattransports the autoinducer into the cell, wherein the cell produces adetectable signal in response to the first autoinducer; measuring theresponse of the cell to the first autoinducer in the presence andabsence of a test compound; and comparing the responses to determinewhether the test compound modulates the response to the firstautoinducer.
 29. The method of claim 28, wherein the cell has beengenetically engineered to increase expression of the transporter. 30.The method of claim 28, wherein the transporter comprises at least onepolypeptide comprising a sequence selected from the group consisting ofSEQ ID NOs.: 37-40 and a sequence having at least 25% identity asdetermined through use of FASTA version 3.0t78 with the defaultparameters to one of SEQ ID NOs.: 37-40.
 31. The method of claim 28,wherein the transporter comprises a complex comprising each of the aminoacid sequences of SEQ ID NOs. 37-40 or amino acid sequences having atleast 25% identity as determined through use of FASTA version 3.0t78with the default parameters to each of the sequences of SEQ ID NOs.:37-40.
 32. The method of claim 29, wherein the cell comprises at leastone vector from which one or more polypeptides included in thetransporter are expressed.
 33. The method of claim 29, wherein the cellcomprises a mutation that increases expression of the transporter. 34.The method of claim 33, wherein the mutation is in a gene encoding arepressor that reduces expression of the transporter.
 35. The method ofclaim 34 wherein the mutation is in a gene comprising the sequence ofSEQ ID NO:
 28. 36. The method of claim 34, wherein the mutation is in agene comprising a sequence having at least 30% identity to SEQ ID NO: 28as determined through use of BLASTN version 2.0 with the defaultparameters.
 37. The method of claim 34, wherein the mutation is in agene encoding a polypeptide comprising the sequence of SEQ ID NO: 36 38.The method of claim 34, wherein the mutation is in a nucleic acidcomprising a sequence that hybridizes to a probe comprising at least 20consecutive nucleotides of SEQ ID NO: 28 in 6×SSC at about 45° C.followed by one or more washes in 0.1×SSC/0.2% SDS at about 68° C. 39.The method of claim 34, wherein the mutation is in a polypeptidecomprising a sequence having at least 25% identity to SEQ ID NO: 36 asdetermined through use of FASTA version 3.0t78 with the defaultparameters.
 40. The method of claim 34 wherein the cell furthercomprises a mutation in a gene that inhibits the production of theautoinducer.
 41. The method of claim 40, wherein the mutation thatinhibits the production of the autoinducer is in a luxS gene.
 42. Themethod of claim 41, wherein the mutation that inhibits the production ofthe autoinducer is in a nucleic acid comprising a sequence selected fromthe group consisting of SEQ ID NOs: 1-9.
 43. The method of claim 40,wherein the mutation is in a nucleic acid comprising a sequence havingat least 30% nucleotide identity as determined through use of BLASTNversion 2.0 with the default parameters to a sequence selected from thegroup consisting of SEQ ID NOs: 1-9.
 44. The method of claim 40, whereinthe cell further comprises a mutation that inhibits the detection of asecond autoinducer that is an acylhomoserine lactone.
 45. The method ofclaim 44, wherein the second autoinducer isN-(3-hydroxyacyl)-L-homoserine lactone and the acyl group comprises 4-12carbon atoms.
 46. The method of claim 45, wherein the acyl groupcomprises four carbon atoms.
 47. The method of claim 44, wherein themutation that inhibits the detection of the second autoinducer is in theluxN gene.
 48. The method of claim 28, wherein the autoinducer is theautoinducer-2 produced by Vibrio harveyi.
 49. The method of claim 28,wherein the autoinducer is a pentanedione.
 50. The method of claim 49,wherein the pentanedione is 4,5-dihydroxy-2,3-pentanedione.
 51. Themethod of claim 28, wherein the cell belongs to a species selected fromthe group consisting of S. typhimurium and E. coli.
 52. The method ofclaim 28, wherein the cell belongs to a species selected from the groupconsisting of Haemophilus influenzae, Helicobacter pylori, Bacillussubtilis, Borrelia burgdorferi and Vibrio cholerae.
 53. The method ofclaim 1, wherein the cell is a Vibrio harveyi cell.
 54. A method forscreening a candidate compound for the ability to bind to a transporterthat transports an autoinducer into a cell, wherein the autoinducer isnot an acyl-homoserine lactone and can interact with the Vibrio harveyiLuxQ protein thereby inducing expression of a Vibrio harveyi operoncomprising the luxCDABE genes, comprising: contacting the transporterwith the candidate compound; and determining whether the compoundspecifically binds to the transporter.
 55. The method of claim 54,wherein the compound comprises a detectable label.
 56. The method ofclaim 54, wherein the transporter comprises at least one polypeptidecomprising an amino acid sequence selected from the group consisting ofSEQ ID NOs.: 37-40 and a sequence having at least 25% amino acididentity as determined through use of FASTA version 3.0t78 with thedefault parameters to one of SEQ ID NOs.: 37-40.
 57. The method of claim54, wherein the transporter comprises a complex comprising each of theamino acid sequences of SEQ ID NOs. 37-40 or amino acid sequences havingat least 25% amino acid identity as determined through use of FASTAversion 3.0t78 with the default parameters to each of the amino acidsequences of SEQ ID NOs.: 37-40.
 58. A method of screening a candidatecompound for the ability to modulate the binding of an autoinducer to atransporter, wherein the autoinducer is not an acyl-homoserine lactoneand can interact with the Vibrio harveyi LuxQ protein thereby inducingexpression of a Vibrio harveyi operon comprising the luxCDABE genes,comprising: comparing the binding of the autoinducer to the transporterin the presence and absence of the candidate compound; and determiningwhether the the extent of binding of the autoinducer to the transporterin the presence of the compound increases or decreases relative to theextent of binding in the absence of the compound.
 59. A method ofscreening a candidate compound for the ability to bind a polypeptidecomprising: contacting a polypeptide comprising a sequence selected fromthe group consisting of SEQ ID NOs. 37-40 and a sequence having at least25% identity as determined through use of FASTA version 3.0t78 with thedefault parameters to one of the sequences of SEQ ID NOs.: 37-40 withthe compound; and determining whether the compound specifically binds tothe polypeptide.
 60. An isolated bacterial strain comprising a mutationthat inhibits the transport of an autoinducer that is not anacyl-homoserine lactone and that can interact with the Vibrio harveyiLuxQ protein thereby inducing expression of a Vibrio harveyi operoncomprising the luxCDABE genes.
 61. The bacterial strain of claim 60,wherein the mutation is in a gene selected from the group consisting ofthe lsrA, lsrB, lsrC, and lsrD genes.
 62. The bacterial strain of claim61, wherein the strain is a Salmonella typhimurium strain.
 63. Thebacterial strain of claim 62, wherein the mutation is in a sequenceselected from the group consisting of SEQ ID NOs.: 29-32.
 64. Thebacterial strain of claim 63, wherein the mutation is in a gene encodinga polypeptide comprising a sequence selected from the group consistingof SEQ ID NOs.: 37-40.
 65. The bacterial strain of claim 63, wherein themutation is in a nucleic acid comprising a sequence selected from thegroup consisting of a sequence having at least 30% nucleotide identityto one of SEQ ID NOs.: 29-32 as determined through use of BLASTN version2.0 with the default parameters.
 66. A bacterial strain thatoverexpresses or underexpresses a polypeptide comprising a sequenceselected from the group consisting of SEQ ID NOs. 36-43 and a sequencehaving at least 25% identity to one of SEQ ID NOs: 36-43 relative to awildtype strain.
 67. A bacterial strain that overexpresses orunderexpresses a polypeptide comprising a sequence selected from thegroup consisting of SEQ ID NOs. 36-43 and a sequence having at least 25%identity to one of SEQ ID NOs: 36-43 relative to a wildtype strain. 68.An isolated or purified nucleic acid comprising a sequence selected fromthe group consisting of SEQ ID NOs.: 28-35 and a fragment comprising atleast 20 consecutive nucleotides of one of of SEQ ID NOs.: 28-35.
 69. Anisolated or purified nucleic acid comprising a fragment of one of SEQ IDNOs.: 28-35 that encodes a polypeptide that can facilitate the transportof an autoinducer into a cell, wherein the autoinducer is not anacyl-homoserine lactone and can interact with the Vibrio harveyi LuxQprotein thereby inducing expression of a Vibrio harveyi operoncomprising the luxCDABE genes.
 70. A recombinant vector comprising asequence selected from the group consisting of SEQ ID NOs: 28-35operably linked to a heterologous promoter.
 71. An isolated or purifiedprotein comprising a sequence selected from the group consisting of SEQID NOs.: 36-43 and a fragment comprising at least 10 consecutive aminoacids of one of of SEQ ID NOs. 36-43.
 72. An isolated or purifiedpolypeptide comprising a fragment of one of SEQ ID NOs.: 36-43 thatencodes a polypeptide that can facilitate the transport of anautoinducer into a cell, wherein the autoinducer is not anacyl-homoserine lactone and can interact with the Vibrio harveyi LuxQprotein thereby inducing expression of a Vibrio harveyi operoncomprising the luxCDABE genes.
 73. An antibody that binds to apolypeptide selected from the group consisting of SEQ ID NOs.: 36-43.